It's a lot easier and fashionable trend to abuse something like Scientology for it's beliefs than it is to have a go at one of the more established religions.
This is true. However, Germany HAS also been going at more established religions when their practices violate laws.
For example, female genital cutting. Though not a part of Islam, though it predates Islam, it is practiced by many Moslems, and has definitely gained a religious dimension. It's still illegal in Germany, though. It's not covered by religious tolerance, as the practice breaks German law.
"Religious freedom" does not excuse the breaking of laws. I can't create a cult based on human sacrifice, and hope to have it respected due to religious freedoms.
Stalking people, and preventing people from getting medical treatment they need, also goes against German (constitutional) law. As such, Scientology is perceived as a danger, and Germany has the kind of government that does warn its citizens from dangers. Does this make it a nanny state? Possible. But as it does the same in regard to cigarettes, alcohol, drugs, unsafe driving, unprotected sex .. it's hardly an inconsitency.
Either way though, nazi metaphors are fun, but completely wacky here. The prosecution of Jews in Germany had nothing to do with Jewish religious practices in any way breaking German laws. At NO point was what happened then, in any way, comparable to this. There is no slippery slope.
If the persecution of Jews in Germany started with the Nazis warning people that circumcision can cause infections, you'd have a point. Alas, it didn't.