I believe we are wandering off. The point I was trying to make is that the word of priests weight little compared to that of a Duke. Because the balance between the feudal hierarchy and the ecclesiastical hierarchy is disrupted by our modern view on religion.
That's not the problem of the game. It's a problem with the players. You need to find a way to fix that in-game. I have seen it work in-game, so I know it can be done.
In my opinion, the Church must rule the feudal hierarchy, and not the other way around. The example you gave requires the full support of the feudal hierarchy, meaning they voluntary want to get rid of the Duke. Then the initiative comes from the crown, 'asking' the church to charge the Duke with heresy and to undo him from his feudal seat.
But if the Church finds reason to believe the Duke is a heretic, then there is no way to pressure the crown because the common nobility will always be more loyal to the feudal than the ecclesiastical hierarchy.
If it can't go the other way, with the church pressing charges of heresy (or whatever) against the duke, and making it hold up against the feudal hierarchy, then your church is not strong enough, and has no business trying to kick out the duke.
What you're describing isn't a problem with religion itself. It's a problem of the players' attitude toward religion. Religion can be very powerful, if the players are willing to go along with it. It is up to the religion's players to convince the realm's players to do that. But really, that's the same that it is even with any council positions, too. If the people in the realm don't want to go along with the council, they can ignore them or kick them out of office.
This is not something that game mechanics can fix. It is something that will have to be solved by player attitudes.
