Do all of the organisations of that religion need to be dangerous to warrant a ban on the entire religion or just some clubs? The biggest clubs, the most clubs, whats the criteria here? What about people practicing that religion that do not belong to any religious organisation?

Again you are proposing banning an entire religion, that means places of worship, religious texts and items and removal of any public display of these religions because they are deemed as dangerous as nazis. So it stands to reason that any building or statue that displays the same religious symbols ought to be demolished or vandalised to the point where it can no longer be recognized as a building of that religion.

How should a government judge a religion as worthy of such persecution as the nazis?

edit: maybe via an example. Tell me which religions you want the government to ban and why.