The name is burnt. They still are a company with business interests. While their interests might align today with the open source community this doesn't have to be so tomorrow and there is no resistance internally to burn these bridges they are building today.
It doesn't solve the number one issue: External references to your project will all still point to github.com since that's where the project homepage (aka README.md) is.
If GitHub does get sold to MS and I end up moving to GitLab, I'll probably push one last commit to the GitHub repo adding a header saying the project has moved, with a link to the GitLab repo. It's not perfect, but it wouldn't be too bad.
Until MSFT/GitHub does what Sourceforge.net did - taking over project sites from projects which moved away and adding malware (adware/spyware) into those ;)
(I believe with all critique on Microsoft they aren't as bad, but want to exemplarize the risk)
It might just be cleaner to close the github repo and when other projects find a 404 where it used to be, they'll have to use super detective skills (i.e. Google it) to find the project's new home. And if they can't find it that way, then nothing of value was lost. (Yes, yes, I know it's more nuanced than that, but if you wanted permanence, you'd be hosting on your own domain, right?)
I expect Google could be convinced to accept certain files or metadata in a README as equivalent to a 301 permanent redirect, meaning searches will remain effective. That would account for a lot, especially if Chrome begins to honour it.
I wonder how Microsoft can manage to commercialize all the projects on GitHub. Maybe by providing an universal installer that works through the Windows Store. Maybe by adding a few mandatory patches to each project that improve compatibility. Maybe by making a much improved version of Git with a proper GUI interface. The possibilities are endless!
That's probably the whole point of it. Ask yourself daily: WWMD? "What Would Musk Do?"