it wouldn't alter balance significantly, since 1) AI are mostly useless anyway and 2) they are supposed to be able to repair themselves anyway, they just don't always.
I find myself slightly disagreeing with that. The AI is not 'mostly useless'. Especiallly not when you are playing on Insane, where both the friendly and the enemy AI are better at what they do, and where you are just as vurnrable as your AI squadmates (at normal, you have 1,5x armor or so, and there's a limit on how many fighters will attack you at once. This isn't the case on insanity).
Oh, as a side question: Does anyone know what effect ordering your squadmates to depart has? I tend to do so when they are so badly damaged they won't make the next fight, and noticed that the times I started doing that I gained ranks a bit quicker, although I don't know if it just me getting better or it having an actual effect (I know calling reinforcements in makes you lose points, telling them to depart might just help gain them).