It's not a distaste for spiritualism, it's just a cultural and religious trope. A lot of folklore in various east asian religions revolves around spirits and gods being born from normal people. They sometimes go corrupt, and have to be killed by heroes who sometimes become gods themselves.
I can see the argument about demystifying the FFXIV pantheon, but I think that's kind of what the game is all about at it's core. The scions are made up of almost all uber-educated scholars above 99% of the world. The group started as the "circle of knowing" and most of what we do involves trying to turn magic into a science.
