AT&T have been putting themselves through some real contortions to argue that their limiting of Facetime access on their cellular network to those people that sign up for their new mobile share plans. Arstechnica's Nate Anderson has a good assessment of AT&T's position here: http://arstechnica.com/tech-policy/2012/08/att-have-you-no-shame/
What is interesting is how AT&T justifies their position in relation to Net Neutrality by arguing that subscribers can download alternative apps for video calls.
So if Apple wanted to throw AT&T a curveball they only have to do one thing. They take Facetime for iOS, pull it out of the core iOS application set and make it a separate downloadable App on the App Store. By AT&T's rules Facetime would be the playing on the same level Playing field as Skype and other video calling apps in the App Store.