We spent a LOT of time actually putting in sidebars to allow for ease of homebrew use.
You will be able to use 95% of the crunch (game material) such as domains, spells, new classes, feats, etc with little to no modification. There are sidebars for every new or alternate material describing how to them in a non-gothos campaign. For example, all the true path's (alternate abilities based on god for rangers, druids and paladins) have a listing describing what pre-requisities a non-gothos god would need to use them. Another example is a sidebar describing how to determine what 3rd party spells fit into the shaman and witch classes.
For the panthoen and pagan gods, each is fully described. It would take little effort to replace their conflicts and secerts regarding a gothos god for one of your home brew if you want to introduce them. For example, The Northwind (a pagan spirit) fights often with Tristar, a god of the sky. If you have a god of the sky, you can swap names and use the northwind with no real effort.
If you do not want to introduce new gods, take note that all the gods have NPC's and magic items fully laid out for use in games.
Have an evil god of pestilence in your world? You can use the NPC High Priest of one of the described minions of Gothos's version in your game with a name change.
Hope that helps,
See ya,
Ken Shannon
