Good question fusangite... I think, perhaps, we might not want to get too specific about gods... other than the minor deities that have been offered thus far.
A couple of ideas...
Temples could be placed on the map with simple... generic descriptors for the type of god... War, Love, Fertility, Hearth, Nature, etc. This allows any DM to use any pantheon they choose for the gods.
Perhaps there is a section of town... a small square where adherants (sp?) of foreign gods congregate... There might be several small shrines to a multitude of foreign gods. Mor's End, being a caravan pit stop, probably has plenty of foreigners wandering about. If one large group migrates to the area, that group might then move their worship from "Shrine Square" to a proper building...
Well... charts and graphs beckon... I must go back to work... bleh...
--sam