I'm pretty sure, though not 100% sure that you can avoid the Papacy and Horde by simply basing your mod on VI instead of MTW. I'm not 100% sure how this works but the Samurai Wars mod doesn't have the Papacy faction. It may avoid the GH by simply not covering the year 1231, but I think it also avoids the Horde by being based on the VI campaign. I think some other mods take the same approach. If you try to remove the Horde from the MTW campaign then I'm pretty sure it will crash the game when 1231 arrives - even if you do it thoroughly. I can't be certain though as I've never tried this myself.