I believe it states in the spell that Awakened creatures can begin taking class levels. But it also negates the Animal Companion aspect. Does he plan on taking Leadership and keeping it as a Cohort, or was he unaware of this part of the spell?
Well, you can see the spell for yourself here.
The spell does not state specifically that the awakened creature can take class levels. It says that an animal becomes a magical beast. However, the Bestiary gives advice on how to add class levels to monsters, and there is plenty of precedent for creatures with greater-than-animal Intelligence taking levels.
I've done it many times with various creatures. It is not game-breaking. Go for it. But remember, as Joex said, the bird cannot be an animal companion anymore (though it remains friendly).
If this animal is an Animal Companion or Mount class feature... it stops being that when Awakened. It becomes fully self aware and becomes its own individual. It is an NPC at this point. It is no longer his, or part of his character in any way.
Be careful when Awakening... it often bites you in the rear. Or, they're free to do so if they want to, at any rate.
It's not a bad way to make some interesting NPC allies, though, and allies are always useful.
Also, note that the last creature you awaken does help you to the best of its ability, and those you've previously awakened are still friendly. So it isn't like they just say "thanks, now sod off".
