I could make the same concern for a bunch of other companies who were to buy GitHub. Indeed, my main concern with GitHub being bought by anyone is the uncertainty of its future, and the fact that it no longer will be 'neutral' ground, so to speak.

It's not in particular Microsoft that concerns me (although their embrace of Git, this seems inevitable for a company like that, considering its history), but that GitHub is now losing its appeal; it being independent from the big players.