"If the gods didn't exist it would be necessary to invent them" :D I haven't commented on this before, but the "revelation" being made in the first game of a series, that "the gods are fake", "it's all a conspiracy", is one of the most notorious instances of a story writer shooting himself in the foot. That's first.
Second, educated people in this "low-key fantasy"(!) world behaving as if revealing this conspiracy would bring about a societal crisis, a breakdown of institutions or even major outrage, rings false in every way imaginable:
An unprejudiced recipient of this story expects that characters would behave rational within the reality of this fantasy world, and expecting aforementioned crisis to happen as a result of simply airing the message "the gods are fake" would be a highly irrational expectation for a character such as Thaos to have, let alone for others who are in on the big secret.
I find it really mind-boggling that anyone with a good general knowledge of history wouldn't laugh his ass off at such a proposition for a main plot hook. Let's see, what is realistically expected to happen if someone starts shouting at the top of his lungs that the gods aren't real, in an actual low-key fantasy setting:
1. People will make fun of him in taverns and on the streets
2. Should he gain enough traction, churches will persecute him for heresy and he will be considered a danger to all for his speeches "angering the gods"
3. In the best-case scenario, from the perspective of this fighter for truth, he would become the leader of a heretical cult.
So, no societal breakdown, no crisis, no angry mobs in front of temples. From what I remember of Pillars' development history, I think the story was chosen after they spent lots of time tinkering and couldn't decide what to run with. Read: it was one more aspect of the game that was half-assed due to kickstarter promises and time/budget constraints.
I could go further into why such a plot hook is absurd, but I really don't think there is a need for that.