GitHub is stupid valuable for MS, and will make their dev tools offerings much stronger (TFS is a dog, bringing GitHub Enterprise into MS Enterprise support & sales cycle is gonna make a loooot of scratch). But the value of the GitHub community persists only so long as the community is present. MS can't start destroying Open Science, because Open Science will be open any- and everywhere.
Frankly, disciplines should be creating their own community hubs and portals based on Git and the publishing standards of GitHub: leveraging GitHubs infrastructure and standards while capturing and engaging with the relevant users. That way they can always migrate and maintain the community.
Besides, even cynically MS is more likely to do a bad job of community management trying to upsell related services moreso than poop on things for the sake of pooping on them. If it becomes offensive you'll have a nice window to find a superior collaboration hub.