Although i am cynical about the news, one thing in their defence is that not all of their take overs have been bad, I mean I know we have seen stuff die in their hands like Skype, Lionhead (though Peter Molyneux can take some credit), Nokia, TrueSpace and so on. Hotmail (as an example) remained popular for years and more recently, LinkedIn, which I didn’t even realise until recently was now owned by Microsoft and I don’t believe anybody lost their heads over it.
So it could not be that bad. I see no reason to jump ship yet, as you say, wait until something bad happens. A number of services out there are already integrated with GitHub so it seems premature to flee (but I have heard of boycotts already). Granted it raises alarm bells for me as MS has a reputation over its takeovers, but no guarantee it’ll be a flop...unless so many people leave out of reaction to make it a self-fulfilling prophecy.