Yeah, I seriously doubt Microsoft will twist Github into something unpalatable for developers any time soon. It's possible, I guess - Google's doing a great job killing the experience for Youtubers. I keep hearing rumors of a several who are working to build a distributed video hosting platform... again.
At least we have somewhere to go if it happens to Github.
Anyway, I think the most we can possibly worry about for quite some time is just the fact that it's ... unsettling to see that Microsoft owns the world's dominant source code management platform.
It's sort of like, I wish they'd give me reason to leave, but I know they won't.