I find the "horrified at God is Dead" trope to be not particularly interesting, and at least the initial game's presentation of Eothas and his actions to be pretty off-putting. As in, they specifically took the deity I normally would have liked most and made him something monstrous. Also atheism is true and all believers are deluded fools enslaved to an ancient conspiracy...not really "for me." Having read up on the sequel, it sounds like it gets somewhat better, but not in a way I find very compelling. Whether the gods are mere machines or huge piles of souls condensed in giant soul gems or organically-bred wonders of biotechnology...doesn't really matter to me. They're all machines (of whatever construction) created by humans, and any belief in them is thus axiomatically hollow. Characters like Edér make the situation worse, not better.
I much prefer the agnostic approach. No one knows and it is always a choice. I encoded this into my own home game. A powerful deity-like being is known to exist, whom the Safiqi priests call The One. The One cannot prove unequivocally that it is the one true God (and its servants claim They would not, even if They could). So it's ultimately a choice for each person: to decide, based on inherently incomplete information, which path seems to be correct. There is no proof that cannot ever be questioned, no independent objective facts that can be accessed even in theory.