A good system to make religion actualy do something more beneficial then setting alot of "kill on sight" flags for foreigners would be to give each civ it's own pantheon, possibly sharing it with a few others. Each pantheon contains several deities. Each deity has a sacred object related to it's specialty(for the god of farming this could be a millstone), a sacred day(for the above god of farming, this could be 1st day of spring), a blessing it can give if you worship it enough(randomly adding a beneficial tag or removing a negative tag to something relevant, our god of farming could make wild strawberries grow underground) and a curse if you don't worship it enough(tampering with the soil quality in your farms for example)
At the start, your fortress only worships the general pantheon and it's generic atributes(mostly related to the upper deity).
-You can keep it that way to maintain friendly relations to everybody but no specific benefits(jack of all trades, master of none)
-You can go atheist, stepping on alot of divine and priestly toes but gaining full independance otherwise.
-Specialize in a cult of a specific deity, gaining the bonus of that god but also the disadvantages.
Once more detailed politics are in, these could all have additional effects(worshipping Frillypaddles, goddess of forestfires won't make you alot of elven friends) but for mow i eagerly await the Army Arc.