We (in the United States) give churches little
power over government at all - other than the power individual voters have -
which is still considerable.
We give the government little power over churches, but we must give it some. If a church, for example, began human sacrifice, we could stop that - no matter what they said their god had told them.
In trade for that amount of power of government over churches, we allow a small power of churches within (but not over) government. "In God We Trust" on the money, for example.
If we gave the churches absolutely NO power, it could be argued that government could also have NO power over them. We couldn't live with that. Religion with total freedom is bloody awful.