I agree, my biggest concerns are:
1. What is happening to Atom? I have tried VS code and don't really like it due to the difference in how the 2 systems are designed to work (Atom being more "plugins are king", VSCode being more "kitchen sink included by first-party"). I'd hate to see my favorite editor lose it's major backing. If MS makes a commitment to continue to develop Atom, or they work with someone else to "transfer" development over to them in a way that's not half-assed, it would go a LONG way toward solidifying the trust they are trying to build (at least to me).
2. How will other companies who are hosting on GitHub react to this? Will Facebook/Google/Apple start pulling their code from GitHub? Will we go back to having to learn how to contribute to each project individually?
There's definitely major benefits for diversity in this area (meaning not having the vast majority of projects on one platform), but I'm hoping we (as developers in whole) don't throw the baby out with the bathwater here.
GitHub has by most accounts helped bring in a renaissance of open source software. It's never been easier to contribute to FOSS at any level, and I'm hoping we don't lose that as everyone diversifies where they host their source code...