People legitimately criticize Github for creating artificial centralization of open source software & having a dysfunctional internal culture, and for being a for-profit company. Microsoft’s acquisition may not make any of these things worse, & won’t make them better. But, there’s a really specific & practical reason people not already boycotting github have begun to consider it in response to the Microsoft acquisition: Microsoft’s history of using deals, acquisitions, & standards committees as anticompetitive tools.
Github was never going to do much of anything beside host your projects, and since hosting your projects is its main business, it’s not going to do nasty things like delete them. Microsoft, however, is absolutely willing to do that kind of thing if they decide they can get away with it. History bears this out — some of it recent. Microsoft hasn’t been able to do it to the likes of IBM or Netscape since the 90s, but only because their complacency over the PC market has prevented them from being able to successfully branch out into phones or servers; however, they have been happily performing their embrace-extend-exterminate tactic on open source projects for the past fifteen years.
(Note: If Github got as big as Microsoft & had side hustles as profitable, they would do the same thing. This isn’t about particular organizations being evil — capitalism forces organizations to act unethically and illegally by punishing those unwilling to break the law.)