It wouldn't be that hard. Tim and I actually worked something out once that would adjust sympathies of regions to other realms, based on the predominant religion present each region, and the official views toward that religion. This was back when Westmoor and Ibladesh were federated, while the predominant religion in each realm considered the other religion to be evil. So, if Westmoor's regions followed CoH, and Ibladesh's followed CoI, then Westmoor's peasants should have an overall negative attitude toward Ibladesh, and resist being allied/federated to them. Given the information that is already available to the game, it's not hard to do. Tim whipped up a script to show it all in table form. From there it's just a matter of determining the magnitude of the effect desire.
When you put it that way, then I guess it doesn't sound all that hard. What to do of pagans, though? And basing it on religion only would both seem abusable and non-representative (The realm on Evilstani used to loot our lands all the time, but hey, New Evilstani was just formed, and we had converted a lot of their peasants, so they must be great guys!).
