Real talk: with the landscape as it is today, I think it was the best landing place for GitHub. Satya Nadella's Microsoft is pretty heavily committed to not losing your trust and we all know if that we mess this up that we lose everyone's trust forever. From my perspective (I don't know anything more about it than you do) this acquisition was about acquiring more good will from developers, really cementing our new stance of being a developer-first company.
What you could be worried about is what happens post-Satya Nadella (again, I don't know anything more than you do, just speculating.) Companies change and maybe some future CEO wants to monetize the hell out of it and ruin it in the process. But for now, for today, I think Satya Nadella and Nat Friedman are going to GitHub in a great direction.