The Church can avoid any such debate by simply not registering as a 501(c)(3). Nobody forces them to.
I do think that (non-registered) churches should pay taxes just like the rest of us. There's no such thing as a free pass for churches.
Okay, let me put this into layman's terms. Since when does the State have the authority (and while we're at it, from who did they get the authority from?) to require registration of, or to grant "free passes" (or deny them) to ANY church?