It just isn't a concept that makes sense. I think I also have a hard time dealing with the premise of gods doing anything toward intervention in general. But, that said, it's just ridiculous that there is that much confusion.

I personally think that the analects were a great way to tell the story because it does allow for complete misinformation to enter historical record. The authors put the analects in there to deliberately confuse the player. The datalogue is just bad story telling form. It really should have been put into the story better.

But, again, the story just has so many gaps. If the Cocoon Fal'Cie were just trying to wipe out humans because they believed humans were a scourge to existence, I'd believe that more than some silly God idea. Especially because they were created by the maker to build Cocoon, as I understood it, and they did, and so, where did this awareness come from for the Fal'Cie.