I wonder what people would have thought if Github had just disappeared instead of selling to Microsoft? I mean I understand some concern, but this can really only be a good thing for Github in the long run. It isn't like Microsoft was producing a competitor and just bought them to kill them. Honestly, I like this better than Amazon or Google buying them.
The reason this happened is to get a payday for the investors. I'm happy they invested, but when you look at GitHub it is a utility, not a commercial enterprise and should be treated like public transport rather than like an oil company.