I don't care if they kill Github. It's the reverse. I'm worried that they will be successful.
My main concern (having spent about a decade working in MS shops) is that they will try to create a divide between "professional" developers and "hobbyist" developers. Microsoft's fear has always been that their next major competitor will be someone who comes out of their garage.
They have always tried to control the programmers so that these programmers will be dependent upon Microsoft. I was literally forced to use Visual Source Safe on more than one occasion because the company I was working for had a contract with MS which prevented us from using any other source code repository (in exchange for discounts on other MS development tools). At the same time, Microsoft did not use VSS internally, because it was horrible. Similarly, we were always playing catch up with APIs. MS would be using them for 18 months or so before any of the rest of use would get any documentation for them (Ha ha! Source code??? Ha ha!)
So my feeling is that this is the embrace part of embrace, extend, extinguish. If I see an effort to rewrite libgit2, or something similar with extensions, then I will be very worried. The reason I can imagine "Don't worry, it will support the git protocol and any hobbyists will be able to make contributions, but if you want a professional interface to Github it is available on reasonable terms (prick your thumb and sign here)" is because I've seen it many times before.
It's not that MS is the only company that pulls this nonsense. Apple is consummately skilled at it: join our fold and have a privileged place in the walled garden.
Free software is intended to level the playing field. As much as MS has improved, I do not believe for an instant that they wish the playing field to be levelled. GitHub, though proprietary originally had no position where it would make sense for them to try to control developer. Now they do.