Updating to iOS 6.1 disables cellular FaceTime?
It isn't exactly iOS 6.1 and it sounds like AT&amp;T at it again. I updated my iPhone 4S to iOS 6.1 yesterday as well and my Facetime over Cellular is still enabled. I am on a shared data plan, though, which has always - since iOS 6.0 - had the option to Facetime over Cellular. 

I think AT&amp;T's response when you asked them shows who is ultimately at fault here. Even though 6.1 isn't exactly at fault, it is possible that AT&amp;T hasn't fully opened the possibility to Facetime over cellular to users with data packages like yours, and that upgrading to iOS 6 somehow re-instated that until AT&amp;T does better opening it up.