The problem with the idea is that all it will encourage is for people to create more "do nothing" religions to avoid the penalty of not being in a religion, while ensuring that the religion's hierarchy simply leaves the nobility alone. Sure if you get a group of elders that want to enforce their position, that would maybe work, but all you would probably see is a mass exodus from that religion by region lords to a religion that will let them go on as they were.
While what you describe would certainly happen, I think through providing the elders lots of power this would at least put people to put more thought into whose religion goes where.
Of course this leaves us with the realm likely sponsoring a religion where the elders match up with the realm's inner circle. !@#$. Back to the drawing board.
