With a bigger microphone comes greater responsibility.
I am not taking Github's side on this particular issue - but this issue struck a bigger tone (for me)...where I have seen those with a larger microphone (by virtue of who they are) seem to be complaining louder (publicly) in recent history. It could just be that their microphone has gotten louder - but if it has, to a large extent they have a responsibility to be more conscious.
Imagine if Obama complained about the food at a bakery down the street that he went to - that would effectively kill that establishment. As a patron, does he have a right to complain about disgusting food? Absolutely...as someone with the largest pulpit in the world? Definitely not. There are other means he could use to get his message across.
Then again, I am not comparing Obama's pulpit to that of Torvalds, but I think it makes the point sufficiently.