If my understanding is correct, if a game is started without llamabanners, anyone who then wants to use that mod during the game can simply copy and paste the info contained in that mod onto the bottom of another mod that is being used. This issue came up during the Cripple Fight game due to there being three different Atlatnis nations in the game.
But this doesn't work as easily in reverse to my knowledge. As in if the game is started with the llamabanners mod enabled, then you will need that mod in order to access the turn files. So if you want a game in which some players want to use llamabanners and some don't, then the best way is to start the game without the llamabanners mod enabled.
Edit: Here is the post/info that players in the Cripple Fight game could use if they wanted to enable llamabanners (even though the llamabanners mod was not active for that game)
http://forum.shrapnelgames.com/showt...ht=#post687279
Edit 2: Having just re-read that post, the info there is only for distinguishing between the three Atlantis era nations. But the theory itself should still be sound. I am not a modder myself, but I am sure most of the modders on the forums can tell you what info from the llamabanner mod needs to be copied.