The Wisdom penalty of the githyanki may well represent their impulsive personalities, but it makes them especially vulnerable to the powers of their first and foremost enemy. So here is my take to solve this problem.
Please check my feat whether it is good or bad, or too strong/weak (and post suggestions for a better wording of its text, if necessary.). 
Will of Gith
By following the path of Gith the Liberator you do not only hone your fighting skills, but you also strengthen the force of your will to defend your mind against the mental powers of your enemies.
Prerequisites: Githyanki, Iron Will.
Benefit: You add a bonus equal to 1/2 your base attack bonus (minimum 1) on Will saves to resist spell-like abilities and spells (or powers) that affect your mind, such as charm person, charm monster, or mind blast.
Special: A fighter can select this feat as one of his fighter bonus feats.
edit: Yes, it know, that this *technically* isn't an RP topic... but its full of story-related stuff...
I admit, I do find the following ironic:
1) The githyanki racial Wisdom penalty lowers their base Will saves, which is obviously important when fighting illithids.
2) According to 3.0 rules, their 'free' psionic defense, empty mind, actually INCREASES their vulnerability to mind blasts!
They DO have psionic power resistance. This does help against mental domination, but not (in the 3.0 ruleset) against mind blasts.
They probably have developed some ways to get around it. (Psicrystals of Resolve are your friend.) Gith(yanki/zerai/pirate)s also seem more likely than any other race to have access to the Quick Recovery feat, which is really one of the best mind blast defenses out there.
Gith(yanki/zerai) are also psionically aware, which (in 3.0 again) reduces the duration of a mind blast stun from 3d4 rounds to 1d4. That alone does a lot to help one's survival chances.
BoGr Guide to Missile Combat:
1) Equip a bow or crossbow.
2) Roll a natural 1 on d20.
3) ?????
4) Profit!