Carmack left iD because they wouldn't let him work on the sort of stuff he wanted to work on. I see no reason he'd stick around Faceulus as an acquihire; if he's working at Facebook in the future, it's because they're letting Oculus do what it was doing when Facebook bought it.
Contracts can be broken. I really doubt John Carmack has to do anything he doesn't want to do. It will be the canary in the coalmine as far as whether I purchase an Oculus HMD when they release.
I do hate this "winner-take-all" situation where a few tech companies in the US acquire every single cutting edge company.