Scientology is not a religion, it is a cult. I cannot figure out why there isn’t a basic standard upon which we allow the various religions to legally exist. Among the basic requirements should be that it doesn’t attack non-believers and that it does not try to isolate members from friends and family.
Again, the government has no say in “allowing” religions to legally exist. That is a violation of the right of free association. If there are crimes being committed, let those be investigated and prosecuted. Otherwise, you are trying to enforce political thought.
Is there an essential difference between religions and cults? I can't think of any. The term "cult" is largely pejorative.
Religion is a very broad term. The best definition that I can think of is that it refers to a set of beliefs about God or gods, and some kind of worship of God or gods.
Now, from what I understand about Scientology, they do not hold any beliefs about God or gods, so perhaps they can be classified as a non-religious group.