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:

Any opponent attempting to directly attack the warded creature, even with a targeted spell, must attempt a Will save.

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.

1. Make the giant swords harder to use. One giant sword isn't really a threat, and drawing ten of them from whatever extradimensional storage they're kept in is going to take some time. So is putting them back.
2. Make their enemies use the same tricks. If you throw a dozen huge swords at a spellcaster, the caster can easily throw them right back.
3. Set up non-telekinesis-friendly terrain. Maybe the enemy has a source of concealment or cover that isn't easily bypassed at a distance, like Obscuring Mist, or some bushes. Adding a 20% miss chance to those sword attacks is a helpful thing.

Both Mind blast is both a spell-like ability and a special attack.

The DnD3.5 has a category of character/monster properties called Special Abilities. They include extraordinary, spell-like, or supernatural abilities. These abilities appear in the monster entries either in Special Qualities or in Special Attack entry. It depends on the Special Ability function, whether it is used to attack or to defend. So, a character/monster property can be both a Spell-like Ability and a Special Attack at the same time.

To find out how the ability interacts with magic (including metamagic feats) you need to know whether it is extraordinary, spell-like, or supernatural. Whether it is a Special Attack or a Special Quality does not matter.

In your case mind blast is a spell-like ability and its level is not specified, so by RAW:

For creatures with spell-like abilities, a designated caster level defines how difficult it is to dispel their spell-like effects and to define any level-dependent variables (such as range and duration) the abilities might have. The creature’s caster level never affects which spell-like abilities the creature has; sometimes the given caster level is lower than the level a spellcasting character would need to cast the spell of the same name. If no caster level is specified, the caster level is equal to the creature’s Hit Dice.

(emphasis mine) link

I.e. all prerequisites for Quicken Spell-Like Ability monster feat are met

Prerequisite Spell-like ability at caster level 10th or higher.

link

But the description also restricts the level of the spell the spell-like ability imitates. The table in the link above lists 16th level (i.e. 16HD for mind flayer mind blast) for 4th level spell (according to mind blast description it imitates 4th level spell).

You can NOT use Quicken Spell-Like Ability monster feat with 12HD mind flayer Mind Blast. You need at least 16HD.

Whether the property is a Special Attack or a Special Quality matters when applying templates, for example.