I don´t think it´s unbalanced. I´ve played a mystic theurge and the two attributes are just a small part of the problem. Cerebremencers also can´t apply the same metamagic and item creation feats to both classes: they need empower spell and empower power, while a MT just need empower spell. Also, if he picks the feats he need to make an effective psion (psionic meditation, overchannel) and practiced caster/manifester he won´t have any to choose item creation or useful things like Great Fortitude and Improved Initiative.
If you still have doubts, you could speak with the player, saying that you´ll allow it, but reserve the right to clip a spellcasting level if he turns to be too much powerful.