The difficult part about priests siezing regions, and which troops do and don't try to arrest, is that there is no way for a realm to specify *which* TOs it would allow, and which not. Let's say a VE priest joined Astrum and tried to do a TO of an Aurvandil region. There's no way Astrum would sanction that and allow it to happen. So of course we would stop him. Without any way for the game to tell what is OK and not OK, then either way there will be bad situations that don't match what the players would expect to happen.
Maybe have realms have the ability to set a policy on a realm like state religions but not using the state religion mechanic. Could be banned, discouraged, accepted, and encouraged. Accepted and encouraged they would then specifically state if they would condone such an action. Nobles of the faith could have a religion section under politics where they decide if they want to go with realm policy or religion policy on whether or not to arrest priests who do actions like that. If a noble chose religion's policy and a priest of an evil faith an action worthy of being arrested but it was allowed by the realm, the noble's unit would still attempt to arrest because they chose to go with religion's policy. Also if a noble chose religious policy, if the act was done by a priest of a misguided or variant faith it go to realm policy whereas if it was your on faith you would not aid in arresting.
