However, it's not forbidden for MS to change their ways and public image. There is no danger anymore of depending too much on MS tech today. And there's the tactical argument of "the enemy of your enemy" if you know what I mean; eg. these days it's all about about your attention and invading your privacy (and MS also has no clean hands here). But still MS is mostly a software company with a predictable pattern, unlike darker forces able to influence public opinion to a degree not seen before, while MS shilling and astroturfing is easily spotted and amateurish by comparison.
The things I'm more concerned about when it comes to GitHub I've already posted in another story:
They could change the terms of service and essentially drive certain types of projects away. They could limit access to older builds and versions to non-paying customers. They could limit access to verified/signed builds. They could reserve certain rights to your software such as they did with npmjs.com. They could run ads, offer IT staff skill matching and promotions, FizzBuzz-like services, or other LinkedIn integrations. They could come up with clever schemes for offering commercial licensing for open source. They could go after the enterprise package mirrors and policy checkers market Artifactory et al are serving. Not saying they'll be doing that (MS isn't stupid), but given MS is selling mainly to enterprises, there are many creative ways they could make money of it.
Overall, however, I'm not too worried. In fact, I think GitHub has become too much of a monopoly (though I have absolutely nothing against them at all), and I'm always for more choice.