Nat Friedman, who will be the new CEO of GitHub, answered this. He said that both would be maintained as long as there were dedicated users, and that he expected it to be for a very long time.

I expect it could be used to promote Microsoft.

Surprisingly, Atom doesn't even say GitHub above the fold on https://atom.io/ There's an octocat above the fold, but it doesn't mention GitHub until further down the page.