Roles Can Be A Bummer
Making actions/options not available to people can force people out of the magic circle pretty quickly. Sure, roles can help people feel special, but it can go overboard. This does not mean that the rogue shouldn't be stealthy, or that the cleric can't be tank-y, but not being able to use or do something because of an arbitrary class restriction breaks the circle, which means less fun for everyone.
Sometimes, multiple people actually can do the same thing, and that should happen sometimes. If every task you throw at the player characters cannot be accomplished except for 1 person's specialization, it may be a harder adventure than these players (as a group) are fit for. Not that there can't be a situation where you need a particular player to do a something, but that it shouldn't happen all the time.
Perhaps It is a Matter of Perception
So maybe this player is simply just does not imagine the same thing you do. You can try to reinforce what you envision by describing what is going on. Is she/he making informed choices? Does she/he realize what the gravity of the situation, or how her/his character has certain strengths?
Does this player realize the cleric is running around in thick armor, while that player's character is running around in normal clothes? For example, if I think the cleric is running around in normal clothes, and goes into combat and comes out unscathed, I could run in my normal clothes, and also come out unscathed.
If this is the problem, you simply need to be more descriptive! Describe how the cleric is wearing armor, or how the rogue is especially cat-like, and how this player's character is not.
For Games Which Depend On Roles
It may be time to have your other players step up. Have the cleric yell at the other character to stay back, or that the cleric "has this." Alternatively, the cleric may ask "PEASE SUMMON THIS TO HELP ME!" as he charges in.
If the rogue attempts to sneak around, the rogue can give specific instructions; "Can you make a distraction over there?" "Wait here, and if I'm not back in 15 minutes, go get the others to rescue me." Or even: "this looks super dangerous. I don't think you'll make it. We don't want to get ourselves killed, yeah?"
In short, give him tasks, or have the other players give him tasks to help with things. Talking is a free action in combat; use it. This is especially good for players who may be experiencing some mental handicap; it gives them something concrete to act on. It allows them to contribute (which feels great and is fun) without going through negative experiences.
Finally, a player or the DM can specifically highlight when certain actions will require a specific specialization, and who has that training. If it becomes obvious that a task is dangerous and requires training, then most people leave it to the person with the training. The DM can further forbid people without specialization from trying, stating that it's obviously too hard. This is more "hand-holdy" than some people like it, but sometimes people just need their hands held.
Talk About It
Talk with the player about the roles. What is her/his character good at? What should she/he focus on? These other characters have something special about them, what is she/he special at?
Talk about how their character is so good at magic/whatever else, and how they should try to make their magic/whatever else be the solution for the current situation. (After all, we're solving these situations using our strengths, use your strengths to help solve it!)
Tough Love
Finally, you may have to resort to letting the consequences of this player's action happen. Let the events, despite other character's best efforts, happen. Talk about how that character was not focusing on what they were good at, or how their play-style does not match up well with the class they chose. Make a new character that does okay at everything, such as most games' version of a "bard." Note: this does not mean make a character who is rule-breaking and superior to all the others, but one that stands a decent chance at performing many things, and isn't a large risk to the success of most tasks.
This isn't a rules problem, it's a diva problem.
A player who wants the attention of the game focused on him and his awesomeness - by using attacks that let him dominate the battlefield and prevent other players from participating, or by getting upset and hogging your attention (via arguing about the rules) when he can't do so - is a diva, and needs to be handled as such.
Before doing anything, though, you need to determine how much his spotlight-hogging is bothering the other players. Do they get frustrated when he dominates combat and prevents them from joining in? Or are they happy to sit back and let him kill monsters, while they handle other things?
If everyone except you is generally happy with the status quo, then it's probably best to just let it go, and take that into account when building encounters. Give lots of mooks for the wizard to spam with Chain Lightning during combat, then give the other players spotlight time by including whatever type of scenario they enjoy. Let the wizard have his awesome. (Although if you don't enjoy this, then consider winding down the game and starting a new one that better suits your own style.)
Otherwise, assuming the other players also don't enjoy the wizard's behavior, you have a few options:
Enforce Your DM Authority
You're the DM, and you've already used that authority (however accidentally) to create houserules that benefit the players. Now use your authority to enforce houserules that don't benefit the players. When the wizard complains about a ruling you've made, say, "This game uses a lot of houserules. This is one of those houserules. Because of that, the rule you're citing doesn't apply in this case." As others have suggested, it may help to write down all your houserules explicitly, so that when the wizard tries to argue RAW, you can point to a specific houserule if applicable.
This is a socially tricky option, since it's likely to make the problem player feel punished. However, as long as you're consistent, polite, and firm, any tantrums he throws will reflect badly on him rather than you.
Reset the Rules
You say you have a bunch of houserules that mostly happened because you as a new DM didn't know any better, yet your wizard is trying to fight you with RAW. Explain to your players that keeping track of all your accidental houserules is becoming a problem, especially as the PCs increase in level and the math to balance things gets trickier. Then declare all house rules null and void, and require that play operates strictly on RAW from now on.
This option may be technically tricky, depending on the specific nature of your houserules. It may require reworking characters who've been built around the assumptions in the houserules. You may upset some of your other players who've been benefitting from the power-ups the houserules provide. And you'll almost certainly upset the wizard, who from your description will probably feel like he's being nerfed. However, you can point out - without naming names - that since your group is spending a lot of time during game going over the RAW, making sure all the PCs conform to the RAW will reduce that non-game time and let you spend more time actually playing.
Boot the Wizard
If the wizard's arguing is making the game not fun for you and the other players, but everyone else gets along just fine with each other and your houserules, then it may be best to simply stop playing with him. The easiest way to do this is to speak with the wizard privately. Tell him that you've come to realize that his playstyle is very different than that of the game you're running. Explain that this difference is making the game not fun for you (and if you know that other players don't enjoy his arguing, you can add "and others in the group", but absolutely don't name names). Tell him his character will be dealt with respectfully in game, and (if it's true) say that you'd be happy to game again with him sometime in the future, in a setting more compatible with both your playstyles.
This is another socially tricky option, but if this player is sapping all your game time arguing with you about the rules and hogging the spotlight, then it may be better for everyone to cut him loose.
Nuke the Game and Start Over
This is, well, the nuclear option: wrap up your game (could be as simple as "rocks fall everyone dies", or take a session or two to provide closure), then start a new game that either doesn't use houserules, or which has explicit agreement from all players that houserules will be used, and only minimal game time will be given to debating them (e.g., when dealing with a corner case). You can choose whether or not to invite the wizard back to this new game; if you think he'll continue to argue with you and hog the spotlight, it might be best - for your own sanity - to not continue to game with him.
Best Answer
Are you sure there's a problem?
It sounds like the things that your players are doing are pretty legit, and not really overpowered. Remember that using the Violent Thrust option for Telekinesis consumes the spell all at once, and doesn't let you use either of the other options at the same time. The things that you're talking about all sound like sort of underpowered uses of a 5th level spell. I think if might help if I enumerated why each of these uses isn't actually that powerful.
I'll go through the list:
Throwing grenades
There are two ways I can think of to 'throw' grenades with Telekinesis. Either you can use Violent Thrust to quickly toss a grenade up to 130 feet (which would likely ignore any AMFs in the way), or use Sustained Force to move the grenade 20 feet per round for 13 rounds (260 ft). How good these options are depends on how powerful your grenades are. If your grenades are something like a non-magical version of fireball, and do something like 10d6 damage, then the first option is just a short range fireball that ignores AMF, and the second is a short-range fireball that takes up to 13 rounds to land. Neither is particularly impressive, especially since it takes a 5th level spell to do either effect.
Throwing Swords
Again, the power of this option will depend on how powerful lightsabers are in your setting. If lightsabers do 3d8 damage and make all attacks into touch attacks, then this option will be quite a bit better. The calculations that I'm doing here are assuming that you're throwing upsized longswords.
So, a longsword does 1d8 damage, and weighs 4 lbs. You can throw up to 13 objects with a total weight of 325 lbs at CL 13, so your best bet is to throw objects that weigh as close to 25 lbs as possible. Gargantuan longswords are 32 lbs, so you could throw 10 of them and stay in your weight limit.
Now, the table for increased damage based on size stops at 3d6, but we can extrapolate to get the damage value for a Gargantuan longsword: 1d8 -> 2d6 -> 3d6 -> 4d6. Assuming you can somehow get these ten swords out of your pack in time to use them, a 40d6 damage attack is certainly nothing to laugh at.
However, the wizard is going to have a rough time actually hitting with those swords. In order to hit with a Violent Thrust, you need to make a normal attack roll with each object, substituting your casting stat for Strength. Since full casters get 1/2 BAB, that means that a 13th level caster likely has something like a +12 attack bonus for each weapon.
The Monster Creation page says that CR 13 monsters generally have an AC of 28, which means that only two of those swords is likely to hit. With a higher to-hit or a lower AC, you'll hit more often, but it'll be pretty unlikely to hit more than 4 or 5 times with a single attack. A 16-20d6 attack is still pretty awesome, but that's totally in line with what a 5th level spell can do. For example, on a failed save, a level 13 Acidic Spray will do 19d6 damage in an area.
Also remember that these weapons are likely nonmagical, and don't bypass DR. DR 5 or 10 is not very uncommon in the low teens, and would have a large effect on the damage this tactic would do. DR 5 would make a 4-sword hit attack deal 36 damage instead of 56. DR 10 would drop it down to 16.
Breaking through Sanctuary
Telekinesis can't get through sanctuary. The spell description states:
Emphasis mine. Since you need to target an enemy in order to use Violent Thrust or Combat Maneuver, you need to make a will save in order to use Telekinesis on a target affected by sanctuary.
Breaking through Wind Wall
Wind Wall isn't really supposed to counter Telekinesis. Wind Wall is basically intended to stop regular ranged attacks and gases, and smaller flying creatures when that comes up. Wind Wall is a third level spell; it's totally normal for a 5th level spell to be able to bypass or ignore the effects of a 3rd level spell. This is especially true since the use of Telekinesis doesn't stop the Wind Wall entirely, it just lets you ignore the wall for one attack. It might even be more helpful to just use Telekinesis on the guy inside the wall, and pull him out with a Violent Thrust.
It would actually probably be more useful to use Teleport, another 5th level spell, to just teleport your whole party past the Wind Wall rather than using that spell slot to make a single attack through it.
Conclusion
5th level spells are really powerful things. It's pretty difficult to come up with a simple obstacle (and anything that can be made with a single spell is a simple obstacle) that a 13th level party can't bypass by using another spell. There are a lot more broken things that your party could be doing with their 5th level spell slots than throwing things with Telekinesis.
If you really don't like what your party is doing with Telekinesis, then there are some things that could help.