Excuse me.....didn't the Taliban blow up the buddist statues? Wasn't the Taliban both religious and governmental leaders?
That's precisely it. When a government is based on a religion, any religion, the temptation is always there to treat opposition to the government as opposition to God Himself, and if one's enemies are opposed to God...then any depredation is justifiable.
I reiterate: No government is competent to say anything to any person about that person's faith. "Render unto Caesar" and all that. Violent, illegal acts ought to be punished as such, not used as an excuse to suppress any faith, no matter how that faith may disagree with the majority's faith.