To my understanding, the elementary purpose of The Divine Realm in ArM5 is, to give medieval religious life and debate some base work, and the player characters some reason to respect it.
If, even with all the suspension of disbelief they can muster for a RPG, your players are not able to take medieval religious life seriously, you can pity them and think of the lot of work in ArM5 being lost on them. But you cannot force them to play with it.
In such case, you can fall back to the device of a modern morals Dominion, like that Xavi has made up on the spot above. Is it cheap? I should think so. But it is your campaign, so you decide.
Just don't get criticism of an era mixed up with criticism of a RPG. Before lambasting the middle ages, get your facts right. And before modifying a RPG, understand it.