The problem is deeper than that though. Unless you were developing an Editor or a Git hosting service, you were not in direct competition with GitHub. Suddenly a lot of startups will find their private code hosted by a direct competitor. I wouldn’t feel comfortable if I was them.
While it's not a complete 1-1 mapping, I keep thinking of Stac Electronics disk compression lawsuit against MS when it comes to handling source code:
To be honest, even with regards to private repos, I can't see Microsoft reading the source code because that would be a massive law case waiting to happen. What I'm more concerned about is Microsoft trying to integrate more of their own suite into Github. I'm also concerned about the future of Atom; which I specifically chose over VSC because it wasn't managed by Microsoft.
Not that because it happens, it is nice; but at-least at this point the source code access concern is more of a conspiracy theory if anything.