I can actually see some weird corner cases with this logic.
I cast a cure spell and am holding the charge. My "Ally" moves up to me, then away, provoking an AoO. I attempt to attack him with my held spell (which is a threatening weapon, so I can). I make my attack roll - oops, I just healed my "enemy" on his turn.
And it's the weird corner cases that I am thinking of. The reasons to make such an attack of opportunity on an ally are few but I think worth considering, particularly if your character is based as a combat reflex character. The wording of enemy seems very subjective to me and to much is left to the interpretation of a GM (and I'm the GM on this one). I lean towards yes on the AoO on a friend. A lowered defense of a friend is still a lowered defense according to my view. The inputs here so far are great.