Imho, this strikes me more as a similar situation as a primary school kid getting suspended for swearing at school. Sure, freedom of speech technically allows him to say whatever he wants, but at the same time the school is responsible for preventing classes from turning into a profanity-fest.

What's the big deal if Github did delete the repo data from their servers? Isn't the whole point of Git that you can just go and setup an upstream somewhere else with a one-liner? They are merely a free hosting provider among many.

This is not a dispute against the government, so the discussion about censorship and the rights and responsibilities entailed by free speech isn't relevant at all. Remember that the free speech provision is primarily intended to be about citizens' ability to self-organize to defend their constitutional rights if their representatives don't have citizens' interests at heart; it's not meant to be used as an excuse for immature behavior.