Let me be ridiculous for a second:
I start a religion where one of the basic tenats is to convert people to my faith or kill the non-beliving infidels. Of course, I base this on my own interpretation of the Crusades and Inquisition thus believing that this sort of action holds religious validity in any Christian country.
I start my new religion’s Crusade by killing a bunch of people? Does the government have the right and responsibility to stop me and punish me? If so, then we have established that there are limitations on freedom of religion just like there are limitations on freedom of speech or assembly.