Yes, but with scientology, there are several distinct concerns that should be treated separately :

1. the State not discriminating between belief systems
   
2. fiscal status : clearly, Scientology should be taxed as a business, not as a non-profit (as most religions probably would be, as long as the audits checked out)
   
3. mind-control cults, against which the state must provide safeguards, independently of the other two concerns.

I have friends who were briefly members/clients of some motivational-method organisation, which claimed no religious status, and was later dissolved under French anti-cult law.

_{It is rightly acknowledged that people of faith have no monopoly of virtue - Queen Elizabeth II}