This sounds potentially dangerous—if this succeeds, the government may be able to shut down any church which opposes politically correct beliefs (e.g. on gay rights or abortion). The Bill of Rights prevents Congress from passing a law interfering with the free exercise of religion, but doesn’t say anything about the courts doing so.
You make an interesting point that I had heretofore not pondered.
You would think that the very language of the Constitution that you mention would serve to remind the robed-but-naked courtroom emperors that the role of law-making belongs exclusively to Congress and the President.