I'm kind of worried about society deciding which speech is "intolerant", so I'm not completely on board with the idea of treating tolerance as a social contract. That being said, if we could stop a genocide merely by suppressing people's speech, I feel like that would probably be a worthwhile thing to do. That is to say, it feels like the least bad way to prevent a genocide.

Again, figuring out which speech is worth suppressing is a whole other can of worms.

EDIT: note that Jones did have his speech suppressed, and this was done because his speech was causing people to make death threats against the sandy hook parents. I feel like we could classify Jones's speech as intolerant against sandy hook parents, and the same logic applies as for any other type of intolerant speech.