I'm sorry, but that makes no sense whatsoever. Pagan does not mean "atheist without religion". It means they don't follow an official game-mechanics-sanctioned organized religion. There is no way that I would ever support a change.
Quick question: does the "The peasants are unhappy that the local Lord does not follow the majority religion" appear if the majority religion is paganism? I think it would make sense that it does, even when the Lord is also pagan: after all, if it's not organized, it's probably not the same brand of paganism.