Roles Really Aren’t That Important in 3.5
To begin, spells are the most powerful class feature in the game. Dungeons & Dragons 3.5 doesn’t really care much about roles: you will be more powerful the more magic you have. You will never be more powerful going for a non-magic class, even if the rest of your group is already magical. So I call this party a good idea on that account. Unfortunately, you do have some pretty severe power disparity here...
Tier-1s
Wizard and Druid are two of the most powerful classes in the game. All else equal, they can seriously handle a lot more than a group of, say, Monk, Paladin, Fighter, Rogue, and Healer could, at all but the lowest levels of optimization.
Tier-3-ishes
Duskblade and Dread Necromancer are good classes, certainly capable of holding their own. Both are not-awful without spells (Duskblade being nearly as good as a Fighter would have been, and Dread Necromancer having an army of minions), too.
Tier-4-ish
Spellthief is a pretty weak class, but it’s pretty cool. There’s a Trickster variant from Dragon vol. 353 that’s pretty good (lose all but the first 1d6 of Sneak Attack, a fair few skills, and Trapfinding for Bard-like spell progression and adding the Bard spells to your list), though it may make the character less “theif-y” than the player wants.
If possible, you should make Godsblood Spelltheft available to the Spellthief – select Deities or Domains that are appropriate for your setting. This feat gives the Spellthief some nice reliability: if the spell he steals isn’t so great, he can always use one of his Domain spells. It helps quite a bit.
The Spellthief is also the only character with Use Magic Device on his class skill list, and only the Dread Necromancer also uses Charisma. This makes him pretty ideal for the party’s wand-wielder. In particular, your party lacks access to Cleric spells, which are quite good. Wands require a static DC 20 UMD check, which is possible to hit pretty consistently by mid-low levels. Not all spells are good choices for wands, but judicious use of them can give the Spellthief a lot of options.
You actually do have the four roles...
Despite the fact that you don’t really need them, you do in fact have the four traditional roles. The Duskblade is a warrior-type, the Wizard is your arcanist, Druids can heal quite well with lesser vigor (I recommend he gets a wand of it for keeping everyone topped up between fights), and the Spellthief has Trapfinding and the like. Dread Necromancers provide a pretty good “fifth class” here – minions can be whatever you need them to be, and he’s got decent curses and battlefield control.
Of course... the Druid or the Wizard could very easily handle front-lining (Wild Shape, polymorph, etc.), or trap-killing (summons are great for that), or minions (Animal Companion, Handle Animal, summons), or... just about anything else...
Anti-magic Field
Since this got brought up in a comment, some deals with anti-magic field.
It’s a high-level spell.
It’s always centered on the caster.
It’s got a really small radius.
A caster casts anti-magic field on himself, and he’s done.1 Even if a warrior gets an Anti-magic Torc, activating it kills all his magic items, and now he’s in a lot of trouble too. And in both cases, they’ve got to get within range of a spellcaster, activate the AMF (or somehow get in range without magic, but a spellcaster who lets that happen doesn’t deserve the name), and then do something before the spellcaster simply leaves. That radius is way too small to easily pin someone in it, and actions are working against you here.
Casters should be aware of AMF, and build for it. Conjuration (Creation) spells that have SR: No fly right through an AMF – the Wizard’s got a lot of those in Spell Compendium in the form of the orb of spells. The Druid’s Animal Companion, and all of the Dread Necromancer’s minions, can operate more-or-less unaffected by an AMF. The Duskblade does have full BAB and good HP and armor, which means he’s about as good as any other warrior in an AMF. The Spellthief is really the only one who will be largely sidelined by an AMF.
Dead Magic Zone
This is like an AMF, without any of the problems of an AMF. Worse, it’s not even associated with an enemy – it just is. Just, don’t use these. They’re pretty bad for a normal game (arbitrary and asymmetric crippling of characters, with absolutely no recourse), and for this party it would just be a jerk thing to do. At that point you might as well just “rocks fall, everyone dies.”
1 For the purposes of this discussion, I am ignoring the Cheater of Mystra. If you’re seriously playing at that level of optimization, you’re already well out of my league and I cannot help you.
Best Answer
First of all, everyone in the game is entitled to have fun. That’s why it’s a game. If you weren’t having fun, you wouldn’t be playing.
That applies to the rogue as well as anyone else, but ultimately the odd-man-out who is causing problems for everyone else is more wrong than a group that’s otherwise enjoying themselves.
You have to accept, first, though, that the correct answer to the situation may be not playing together. Friends don’t always all want the same thing from a game. I certainly have a few close friends I nonetheless have decided to not play with (and vice versa); the things we want from the game are too different.
For example, someone who constantly wants to go off and do their own thing away from the party, and has personality/alignment conflicts that they do nothing to alleviate and cause problems for the party and make the campaign difficult to continue? That’s the kind of person I would choose not to play with. And I know people like that who would not play with a group that would stop them from doing that. I know others willing to compromise. You need to know where your group stands.
A good place to start, often recommended here, is the same page tool. Using this can give your group a better idea of what everyone wants from the game.
It may be that you are all on the same page, and the rogue player is just better at it. Or it may be that the rogue player and other players want very different things from the game, that the others don’t want characters at the level of competence that the rogue has (or, at least, don’t want to invest in mechanical rules-knowledge sufficiently to create such characters). I’ll address both.
The rest of the group wants, or at least is willing, to get better?
Have the rogue player assist the others, the DM too perhaps, with how to optimize their characters better. Ultimately, this rogue? Really not that optimal. An adamantine weapon is a pretty common tool for mid-to-high-level adventurers, and Agile Riposte is not a good feat at all. For that matter, the rogue is a pretty mediocre class.
So you can potentially catch up to this rogue pretty well if you are so inclined. As DM, favor intelligent, magical enemies, and this rogue will have little response. His Will is probably poor and his Fort is likely little better. For that matter, for all he’ll have above-average touch AC, it still probably won’t be all that good. If you bring heavy magic, particularly on reasonably tough chassis (like, say, a dragon), you may very well overwhelm this rogue, it might be too much.
The rest of the group is not interested in keeping up with the rogue?
This is where you have to start compromising, or agreeing to disagree and play separate games. Lay down some houserules for limiting power; it’s best if you can establish a good baseline of what you expect rather than saying “I’ll know it when I see it”—that’s probably not fair to the rogue player (personally, I probably would walk rather than try to play that particular guessing game). But that can also be really difficult to articulate, especially when new to the game. You don’t necessarily know what is or isn’t powerful (e.g. this rogue, who isn’t all that powerful at all in the grand scheme of things, but seems that way from your perspective), so you can’t accurately describe the power level you want.
Alternatively, you lay down your concerns and problems, and decide whether or not you can trust the rogue player to get along better. Don’t be intimidated by his supposedly-superior experience—his rogue isn’t actually that well-built and his behavior with leaving the party and causing alignment headaches implies, at least to me, a certain amount of immaturity. His experience, whatever it is or isn’t, doesn’t entitle him to dictate the game to everyone else, and it definitely doesn’t entitle him to have his fun at everyone else’s expense.