In all honesty there is really nothing you need to do to remove the gods from NWN. The deity field is written in by the players if they even use it, and it has no real effect on gameplay unless you use it in custom scripts or tokens or something. Feel free to manage the gods however you like.
If you use a custom loot system and custom stores and such just don't add the forgotten realms books.
The only major issue I know of with regards to removing Forgotten Realms from NWN is the item descriptions. Almost all of the items in the standard palette have Forgotten Realms specific lore in them. What I did with the items I wanted to keep was make copies of them in the custom palette and remove/edit the descriptions.
The only other major things are the faerun specific prestige classes like Champion of Torm, Purple Dragon Knight, and Harper Scout. You can supply a custom tlk and edit the classes.2da file to have them with different names though.