Are you arguing that my congregation should be immune from any restrictions being placed on us for worshipping our god by slowly killing everyone around us who does not share our view , because we operate outside of the law ?
What Congress isn't allowed to do is pass a law stating "no religious organizations in the US are allowed to practice human sacrifice." But you still wouldn't be able to appease Xanakto the Moon God because Congress is still allowed to make murder illegal in general, just not exclusively in the context of religious practice.
And, ironically, the reason religious organizations are included at all is the belief that taxing them would provide a means by which governments could interfere with religion in violation of the First Amendment.