My idea for this is that during worldgen a bunch of people could get together and form some kind of organization, such as a knightly order, a guild of masons, a religious sect, or a gathering of necromancers. Essentially, some random person would gain a goal in life, like a desire to heal the wounded, a desire to kill all goblins, ir a desire to teach the true faith. After a while, these people could form an organization, with it's own name, symbol, and titles. Then, people with similar goals to the organization's goals would join said organization. These organizations could be tied to a civ, or be wide reaching, and they would have a headquarters in the site where it was founded. If it became big enough, they could even build headquarters in other sites.
If they felt that the heathen religion was becoming too big, a religious organization could declare a crusade on their enimies, or start an expedition to somewhere, lead an invasion, or start diplomacy. In adventurer mode, you could join one of these and become leader of the organization, and in fortress mode, you could get these organizations to come and visit your fort.
There is also one intersting thing about this, which is that instead of tying gods to a specific civ, civs could start out with no specific religion, and holy groups could start up around pre existing gods, and sites could become tied to specific religions, and civs could start wars over it, etc.
It's an idea.