Yeah, except we already have that. Different sorts of protections come into conflict all the time, and then we have to adjudicate which principle is more important. For instance, the United States is perfectly cool with abridging 2nd Amendment rights on airplanes, because the right to not be killed by some idiot shooting a gun and depressurizing the aircraft trumps the right to carry a gun.

Indeed, guarantees of rights can conflict with themselves. For instance, the 14th Amendment is simultaneously the greatest weapon against and the greatest support for affirmative action, because of the difficulty of fixing past fairness without causing new unfairness.

So your whole premise is badly misguided.

You can criticize religions all you want. Haven't you noticed? Have you ever heard Sam Harris or Richard Dawkins speak (on religion, not neurophilosophy or genetics)?

Besides, the justification for freedom of religion, which you can find if you happen to read Jefferson or other contemporary thinkers, is found in freedom of conscience. That is: we're not going to tell you how you must think and punish you for wrongthink. You get to decide how you think and what you do. We will punish you for antisocial behavior, for harming others, and if you say things that sound like you believe dumb stuff or are a threat, we're going to try to convince you otherwise or intervene when the threat is imminent.

Additionally, I think you overplay the paradox of tolerance, albeit in an unusual way. I've discussed the ordinary ways to abuse the concept in an article here: https://ichoran.medium.com/there-is-no-paradox-of-hatred-fbc3ddeb2500. Though I don't describe your type of overplay specifically, it's still somewhat relevant to your point.