I think it's actually closer to "terrorists should go to prison". Terrorists and other criminals have broken a social contract, and a level of punishment that some approximation of society deems to be acceptable is extracted from the terrorists. This doesn't mean that terrorists don't/shouldn't have some rights. Similarly, thinking about tolerance as a social contract doesn't require stripping anyone who violates this contract of all of their rights.
FWIW I don't actually have a problem with Jones specifically getting in trouble over defamation after getting his day in court. What I have a problem with is the broad notion that it's generally okay to "not tolerate the intolerant" to the point of forcibly suppressing them. The paradox of tolerance is not really a paradox when we're talking about intolerant speech.
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.
