Um, no. Stoning rapists is a religious practice. Those who are protecting them are those who think the First Amendment protects ALL allegedly religious behavior and ties the hands of the government to protect them from that.
You are so literal... have you ever heard of a metaphor?
Protecting the rights we cherish in this country is NOT equivalent to condoning purportedly religious behavior that breaks other laws (i.e., pedophilia, murder, assault). It looks like you are hung up on the freedom of religion clause... are there any other clauses in the Bill of Rights you would like to eliminate? Maybe the right to trial? Looks to me like that is what you are advocating.