They didn't kill Unix or Netscape, not in any way that matters to anyone who actually cared about them.
To return to robin's point: GitHub is a very nicely done web interface to a git repository and the workflows around it. They could certainly mess that in up various ways. But .. you don't "kill" web interfaces to open source technology. Anyone considering their options for git management still has several choices, some of which are self-hosted, some are hosted, some are both. MS might destroy GH or they might make it even more awesome, but there's basically nothing they can do in this domain to "kill" alternatives - just as with Linux, where their efforts to "kill" it (along with most/all of the applications that run on it) have completely failed.
And if they do kill GH (which frankly seems unlikely - more likely is transformation into the steaming pile of mediocrity that is sourceforge), then so what? It's a negative for the world, certainly. But it would no big deal to most projects that use git.