I have, a long time ago, ran into the gods problem and suggested the following:
solving the ingame gods subdungeons could give you an idol, which unlocks a puzzle pack for the explorers guild. Every god gets one and it leads you through the process of unlocking the god and making his alatar available in dungeons (learning how to call upon him and worship him). They could serve as god tutorials which are found in the same manner as new gods are found now, except people would get an incentive (flavour and conten wise) to explore god's behaiviour, and you wouldn't have an exter altar spawning in certain dungeons when you solve a gods subdungeon, or get locked into worship if you decide to take him, thus screwing up your run.
I still think this is a good idea, and quite possibly a necessary one for various reasons. The puzzle packs needn't be large, or symetrical, just big enough to show you the ropes and avoid "I unlocked god X but didn0t want to risk my runs by experimenting with him"