GitHub is to git as Outlook is to e-mail and as Internet Explorer is to the web.
As for how EEE applies to this situation: The situation is consistent with an EEE strategy currently being in the "embrace" phase. It's also consistent with a "embrace, be nice, create win-win outcomes" strategy, but that is not usually Microsoft's modus operandi.
Edit: Actually, I don't think the idea of "Embrace, Extend, Extinguish" even applies to buying out companies. The idea behind that phrase applies to technologies, not companies. You can't "extend" GitHub with proprietary tech, it was never an open source technology in the first place.
If Microsoft starts extending git with new proprietary features that only work with GitHub, _then_ it may be time to start being concerned. As of now though, I don't see how "Embrace, Extend, Extinguish" applies to this situation in the slightest.