I like this general idea, and how thoroughly you described it.
A few thoughts and expansions:
Alternatives to Religion: After a while, "scientific" belief systems or other ones that have no deities may come into being. If there are active gods in the area, this will not occur; if an active deity brings its power to the area, these alternatives will dry up.
Crusades: A group of people with high devotion and decent combat skills in a fairly militant religion will move to kill a group of people who violate their beliefs. For instance, followers of a deity of stone, metal, and war that saw trees as an abomination might purge a fortress of all carpenters and bowyers (woodcutters and wood burners are allowed to live), burn down an elven forest (can you say WAR?), or destroy all wooden houses and other buildings in a nearby human settlement. Obviously, peaceful and pacifistic religions would need quite a provocation to start a crusade--but if they do (say, a peaceful vegetarian religion that is against taming animals watching a large group of elves and tame war elephants and bears destroying a nearby human town and eating a bunch of the slain), this transgression will be great enough that a mighty crusade of farmers and soapmakers and such will rise up and attempt to force the offender to never again violate the precepts.
Holy War: Two differing religions hate each other enough that they send crusades against each other frequently. If they are both in the same entity, this will cause massive deaths; one or both religions might be banned, leading to hidden cults performing inquisitions on the members of the other religion and on the leaders that made it all possible. If two people from the opposing religions saw each other, they would instantly form a grudge against each other, and a fortress whose mayor is one of the opposing religions would sentence members of the other religion to extremely harsh punishments.
New Religions Form: Fortresses should be able to start new religions with FBs, maybe clowns, and definitely sufficiently awesome artifacts and/or high-value stuff (like, -cotton candy large serrated disk- or <<+cotton candy battleaxe+>> or something). These would have properties based off of the thing that spawned them-a religion created by an FB made of stone would consider stone to be sacred, one started around a worm FB would consider worms to be the most exalted of creatures, a religion started by an artifact shield would be based off of defense and peace, and a kobold
cargo cult created by a cotton candy-crafted knife would be militant. (Try not to think of the religions created by a fell mood...)