Separation between church and state is not as clear cut as you think. Rastafarians aren't allowed to smoke weed, for example.
That's a good point. "Separation of church and state" certainly didn't stop the government from interfering with the Mormon church's practice of polygamy.
While those who constantly cite the phrase "separation of church and state" don't want religion interfering with the state, they rarely seem to have a problem with the state interfering with religion.
