If you do this, you'll establish a precedent saying that picking which religions deserve tax-exempt status is acceptable, and then the nightmare begins. Some will say the Catholic church should be non-exempt due to its handling of the pedophile priest scandal. The half of the Presbyterian church that opposes gay marriage will try to non-exempt the half that accepts it, and vice versa. Every religious controversy will lead to a demand to effectively de-churchify a denomination, and the federal government will be the final arbiter of who gets to be a church, in clear violation of the Establishment clause.
So if the scientologists can't be tax-exempt, nobody gets to be exempt. I know Slashdot is full of atheists (I'm one), so maybe a lot of us like this idea. But any politician who proposes it will be demonized by every priest, minister, rabbi, and imam in the country. If you think they believe atheists are assholes now, wait till we try to tax their faiths.
You've got to pick your battles, and this is a bad one. You can't carve this one sect out of the herd of religions without culling the whole herd, and you do not want to be face-to-face with a horde of enraged cattle with pointy horns.