I am now curious if the alignment of a soul is balanced, are there as much water as there are fire? Some other things to consider are does the fountain like one more than the others so those souls become one with it faster?
Some other theorizing is... Perhaps what the fountain's purpose is trying to create a god by purifying all the human souls, humans are capable of higher level thought but is trying to make all of them do it. But humans also are horrible people so, it is creating the Mara. It makes me think that as long as humanity ignores the Mara, even though their souls are getting 'cleansed', Mara are going to stay. They truly just need to accept their evil deeds.
This is reminding me of WoW: Mist of Pandria which also was based off of Chinese lore, the Sha were representations of bad thoughts aka the Mara.