You have the kernel of the answer here. The problem is that "tolerance" is being poorly defined. Am I being "tolerant" of those I disagree with as long as I don't stone them to death? Or do I also have to refrain from saying bad things about them? Or thinking bad things about them?
Murder is to be condemned by society. That's just ground truth. People who murder for religion are murderers. Their actions condemn them, not their religion. Religious motivation is no exculpation. Society has to be "intolerant" of murder and violence in order to be "tolerant" of everyone's ideas.
But there is no way to prohibit bad ideas in the same way as we prohibit violence because people don't agree which ideas are bad. Having whoever wields the biggest stick choose which ideas can't be discussed isn't tolerance, it's censorship.