The Church of Scientology is not a genuine religion, does an honest religion harass former members? Does a real religion forbid adherents from thinking for themselves or physically abuse them if they challenge authority? The real power comes from the church's unprecedented finances, if that were to be diminished (the IRS rescinds the church's status of being tax-free), then the corruption would diminish.
Yes, it is operating for profit as are all religious institutions. All religious institutions should be taxed as they are earning money to pay their staff as well as to fund their missions trips and propagate their religion and own self interests. I guarantee that if you crack open the books of any church, their bottom line would not equal zero (revenues equaling expenses) as they should with a 'not for profit' institution.
Churches should never have been protected in the first place.