In general, religious beliefs can be as free under the first amendment as they come. You can believe in any god or pantheon, or nothing at all in pretty much any fashion. Very free indeed. But is it truly unlimited? So to illustrate, let's take a look at a fictitious religion that is defined by how repulsive it is:
Welcome to the world of Marvel Comics, where people like Reverend William Stryker create fringe cults with bloomy names like Purifiers that propagate hatred, demand genocide and hunt humanoid people for their cause since 1982.
The ideology of the purifiers is simple in its core tenet: People carrying a specific gene shall be found and killed. For that they develop technology to combat those individuals.
While most of the shadow-hidden acts that the purifiers do in the comics are crimes in themselves (abduction, mutilation, murder, genocide...), the Purifiers also are alluded to have a more public-facing side: They preach a rather fundamental offshoot of Christianity, heavily infested with their core tenet to kill mutants.
Now, does that make the religious belief to kill the mutants protected by the Freedom of Religion? At what point does preaching the need for some kind of religious killing from a protected activity to unprotected speech and a crime?