The Constitution supercedes or preempts state law, and the Bill of Rights is universally applied in court. The First Amendment prohibition on the establishment of religion performs exactly as I’ve described it, regardless of what you choose to call it, or how it came to be.

http://www.uscourts.gov/educational-resources/educational-activities/first-amendment-and-religion

I don’t think it’s an unfair comparison. The effect of religious extremism — religious discrimination or religious intolerance — whether enforced by guns or laws or social norms, is always violent and always the same: freedom is oppressed.