You do not appear to actually know anything about constitutional law, civil rights, or the first amendment, so I doubt very much that you would be qualified to explain anything about it to anyone. For example, it seems that in your fantasy world it is a violation of the 1st amendment to NOT grant special privileges to religions.
That's what the phrase about not prohibiting the free exercise thereof is all about.
Indeed, that is the basis of why they are not taxed on their income or their personal property and why Churches indeed can preferentially hire within their own faith and Churches don't have to allow women equal rights to be a Priest.
All of which are special privileges reserved for Religions so as to not prohibit their free exercise.
The 1st prohibits the government from establishing a state religion (with public funding, special privileges and/or penalties on other religions, as was done in England at the time) and secondly, the feds could not interfere with the individual’s right to freedom of worship, and so an important part of the 1st is to protect religion from government intrusion.