You're kvetching about giving the state the authority to destroy religions it disagrees with, I have yet to see why we should acknowledge it as actually being a religion.
You're preaching to the choir condemning Scientology, I doubt you'll find anyone here who disagrees with you there. I certainly don't. That said, can you at least acknowledge the frightening potential for abuse if we empower some Government bureaucrat to determine what is and is not a legitimate religion? How do you draw the line? There's no objective test. You can't go by age, that shuts out LDS, UUism, Wiccans, and a bunch of others. There's a lot of people that would welcome them being shut out, but I'm sure that's not what you're advocating for.
The only fair way to do it would be to treat all non-profit corporations (which is how all churches are incorporated in the US) the same. Leave religion out of it. If you want to tighten the rules for non-profit corporations you might find more support, there's plenty of abuse there, mostly in the secular world, but it's still a tough needle to thread.