I think that's not right, because the reason the company is doing the censoring is to comply with sanctions imposed by the government. If the US says you can't host content praising Iran, and GitHub takes it down to comply, that's a 1st Amendment violation.

However, code seems to be in a strange place, neither clearly speech nor clearly not-speech.

I argue code is absolutely protected speech. The government ran away[1] from a recent case that would've settled the matter conclusively.

[1] https://www.pbs.org/wgbh/nova/article/is-code-free-speech/