When FaceTime was first announced with the launch of the iPhone 4 in 2010, then-Apple Chief Executive Steve Jobs indicated that his company wanted to allow FaceTime calls over 3G, but that Apple needed to "work a little bit with the cellular providers" to bring that capability to users.
Apple already allows some carriers to block or restrict certain functionality on their networks. For example, when iOS 3.0 was released with tethering capabilities, AT&T blocked the paid feature until a year later, with the release of iOS 4.0.
Having experience working at said wireless company, I speculate one of two things are going to happen:
1. AT&T, Verizon, etc are going to make video calls routeable QoS. Similar to how the SMS to iMessage system is seamless, what's likely going to happen is that if you call another mobile device with a video chat application (be it FaceTime or not) it will switch to the native transport at the carrier end.
2. AT&T, Verizon etc are just going to block FaceTime over 3G/LTE by default, and enable it only upon request to prevent unintended data charges, like what happens with international roaming, 1-900, and premium SMS scams.