I think the general consensus is that we want a new, independent org, that genuinely cares about OSS but has the mind to create/maintain a sustainable business model and ensure the long-term success of an OSS platforms is extremely important (and now we'll look to Gitlab and others for that).
Microsoft will, no doubt, have their fingers all over this platform in short order. It's what they're paying for; and it's an extremely smart move (EXTREMELY). Some of GitHubs product offerings have competitors within the Microsoft ecosystem already, which may spell bad times for those long-term. Atom directly competes with VSCode and it simply doesn't make sense to continue development of two, independent, IDEs. Electron utilizes Chromium under the hood, and I'd be hard pressed to thunk Microsoft wouldn't want to try and inject Edge/Chakra into that platform somehow.
It makes good business sense to consolidate efforts once a company is acquired. I give it, at most, 12-18 months before you start seeing major changes to both of those platforms that reflect Microsofts own interests.