sure, they're legally entitled to do whatever they want, but you're failing to consider the most important point:
>You need to consider that GitHub currently hosts a large percentage of the web's open source repositories
would you be happy if google abused its position as the leading search engine to favor right leaning websites over left leaning websites? what about censoring websites that are "offensive" to muslims?
Or what about if your comment were mass-downvoted on HN? Would you be happy?
The censorship card ultimately falls into a relativistic trap - it's always okay to broadcast hate if it's the speech of you or your friends, because you and I can protest ignorance, humor, or lack of wrongdoing, and your more overtly bigoted friends "are good guys when you get to know them." Criticism of such speech, on the other hand, is never okay, and is "the real censorship". You don't even have to invoke a specific ideological dialogue - it is an everyday occurrence in your homes, schools, and bars.
Now, you can go out there and fight and "win" by making your preferred flavor of speech dominant in your spaces, but that just exposes a different facet of this "gem of truthiness" - it doesn't reveal the whole thing, because you still get the same problem, no matter which side you take.
The typical modern response to this is nihilistic or fanatical, but if you really feel challenged by a hostile environment, why not follow the path of the ancients and turn your speech into a puzzle or parable that hides its true intention? If your ideas are good, they will survive the transition and reach the readers who put in the effort to care and figure it out. OTOH if the whole premise is to police the surface aspects of the dialogue and Be Right, then you're speaking politically, not intellectually, and political speech comes with Consequences regardless of the legal environment.
Funny, the same thing seems to happen with the "it's not censorship" card. For example, a while ago a social justice activist got banned from Twitter for death threats against Wil Wheaton, and suddenly all the tech industry folks who claimed sites should ban people for harassment were going after Twitter for doing it because it was an approved social justice death threat.