1. Have a decent fortitude save.
If we assume a fairly optimized 11th level wizard, he's probably got a 27 int or so (+6 headband, starting int 18, +3 bumps from level). So, that's a DC around 24 or so for a 6th level spell.
Let's start with the axiom that disintegrate should usually work on mooks, etc so we're only going to worry about characters within 3 levels or so of the wizard.
Warriors: A single class warrior type will usually have a fortitude save of +7 from class and +2 or +3 from Con and +2 or so from resistance. Total +11-+13 at 10th level. That still fails roughly half the time. So what can be done for the warriors:
1. Multiclass. The single class fighter above has +12 at 10th level with a +2 cloak of resistance and a 16 con. Make him a barbarian2 /fighter 8 and he's +14 normally and +16 when raging. Lots of multiclassing gets silly and is work to put together, but simply adding a second class makes a big improvement. The pious templar prestige class is worth mentioning here because of mettle (a successful save means the disintegrate does nothing) and hexblade and blackguard are worth mentioning because they would get to add their cha bonus to the save.
2. Pay attention to the fighter's race. Making said fighter a dwarf would bump up the +12 save to +15--+19 if multiclassed to barbarian and raging. The extra con and +2 to saves vs spells help a lot. Drow have spell resistance which helps here. Lizardfolk, etc have racial hit dice which generally give you more hit points and fort save per CR than class levels. Using ogre fighter/barbarians pretty much says, "don't bother with disintegrate."
3. Buff your warriors. Something as simple as a low-level cleric casting prayer or recitation or using the nobility domain granted power can quickly boost saves. If we take the starting +12 and add a 7th level evil priest with the nobility domain and the recitation spell, we can add +5 to all the saves. +12 isn't so good against DC 24, but +17 is great.
4. Take feats to improve your saves. Great Fortitude is a good NPC feat. It's +2 to fortitude saves, and, unlike, say, Run, it's likely to come up in combat. And, unlike Improved Trip or Improved Sunder, it doesn't take an action in combat to be useful. Most NPCs won't get to use more than one or two tricks so multiple feats like Improved Trip, Improved Bull Rush, or Improved Sunder are wasted on them. They just need one feat so that they can do their unique thing and then attack once or twice and deal damge before kicking the bucket. If your enemies are cultists, fanatics, or have any obvious religious affiliation, True Believer is a great feat too. +2 to whichever save needs it first. Often NPCs only get a chance to make one or two saves so it's as good as Great Fortitude, Iron Will, AND Lightning Reflexes in that situation.
B. How about your casters? Clerics start out with decent Constitution and make sure they have a resistance item or magic circle vs good/chaos/law as appropriate. Now a 9th level wizard is at +7. What can improve his odds? Pick up Great Fortitude and a rat familiar for the wizard and he's at +12 with a 14 con. Give him the support we discussed earlier and he's good to go. Also consider the spell compendium spells: Major Resistance (Sor/Wiz/Brd 4: +3 resistance to saves for 24 hours) and superior resistance (Sor/Wiz/Brd 6: +6 resistance to saves for 24 hours). That would improve the saves to +13 and +16 respectively and obviate the need for a cloak of resistance or relatively short term magic circle spell. If you do have time for 10 min/level spells, however, heroism grants another stacking +2 to saves. For clerics, conviction is a low level spell that can make a big difference. The luck domain is also worth considering for its abilty to reroll a d20 once per day.
2. Have boatloads of hit points. Remember that raging fighter 8/barbarian 4 with a 16 con? He's got somewhere around 111 hp (131 when raging). Odds are good that he'll survive a disintegrate spell. The wizard is less lucky. If he gets an amulet of health +2 for a 16 con, he still only has 55 hit points or so. (Making him 10th level would give him 61 hit points and if 11th level, 67 hp which would make a difference). Let the wizard cast an empowered false life for an extra 21 hit points or so and a 10th level or 11th level wizard is in the zone where he might survive the disintegrate.
3. Don't get hit in the first place. A standard 11th level wizard has a ranged touch attack of +5 to +10 depending upon dex and buffs. Unless your wizard has point blank and precise shot, he'll also be taking a penalty for firing into melee. So, how can your NPCs exploit this?
A. If they are standard heavy armor types, they will usually have a +1 dex or so. That's a touch AC of 11. If they get into melee and try to keep a PC between them and the wizard, it goes up to 15 and the wizard is firing at -4 for firing into melee. They now stand a good chance of not being hit at all. Now, remember that low-mid level cleric? Magic circle vs. PCs will give a +2 deflection bonus to the NPCs said cleric is supporting. Now it's 13, 17, or 21 (effective) touch AC. That's actually difficult for the wizard. Toss on recitation (luck applies to touch AC) and that's 16, 20, or 24. Haste would help here too if they've a bard or a wizard on their side.
There are also a couple tricks the NPCs could use to support themselves.
A. Combat Expertise. Since this applies to touch attacks, and feeds off the attack roll which you already buffed with recitation and/or nobility domain, it can be a good option. (Not for the raging barbarian though--it'll have to be the fighter/pious templar or fighter/hexblade).
B. Shield Ward (PHB II) lets the NPCs add their shield bonus to touch attacks, and resist grapple checks, bull rush attempts, and trip attempts. Since shield specialization is a prereq, if they've just got +1 heavy shields, that's a +4 bonus to the touch AC making them hard to hit out the gate and very difficult to hit if fully buffed.
For the BBG only: How about a ring of counterspells with disintegrate in it. Everyone can't have one, but it's not out of line for the BBG to have one.
C. Switch to more lightly armored fighters. A fighter with good base dexterity (16+) wearing a chain shirt is only 1 or 2 points easier to hit for the fighters, but is one or two points harder to hit for the wizard.
B. Casters. Blur, Displacement, mirror image, invisibility, and greater invisibility all serve to make the caster difficult to hit. Blink and Greater Blink are even better but blink makes the caster suffer a 20% miss chance on his spells. Clerics can manage shield of faith, and entropic shield.
4. Don't let the caster target the spell. Break his line of sight. Fog cloud, obscuring mist, solid fog, acid fog, freezing fog, etc all prevent the caster from seeing his targets and thus remove the disintegrate threat.
5. Disrupt his spells. It's often good strategy for a support spellcaster or an archer to ready actions to disrupt spellcasting rather than simply to attack. Drop a silence spell, arrow, fireball, or magic missile on the wizard while he's casting and see if he can make the concentration check.