Absolutely. Given what I know about the game's main story and its implications (wasn't there something about the revelations being a threat to kith and gods alike?), it may be that the whole confrontation with Eothas might lead to destroying the pantheon. Or it may put you in the shoes of Thaos, with a new spin on his role and views: Maybe the gods are needed to make the world more bearable, as was the original plan?
Yeah, it would be interesting if the game's developments could potentially serve to challenge the Watcher's perspective on Thaos' choices as they learn more of the secrets of the world/the gods. Tinysalamander touches upon the fact that this has been addressed to a limited extent where companions and their issues regarding are concerned, but there's definitely room for further development.
Also in relation to the end game, I wonder how often the Watcher will have opportunities during the sequel to try to convince others of what they learned within Sun in Shadow.
Good point. In most of my games, I do tend to steer Eder away from devotion to the gods, but I didn't really think about the implications of doing so as they pertain to Deadfire. Based on the examples that developers have provided about companion relationships and how Eder works within that context, it does sound like being pro-Eothas is still one of his centrally defining characteristics, but end game states from Pillars 1 may well influence how open he might be to opposing viewpoints.
While we're at it, one of the earliest updates had this to say about Xoti's perspective on Eothas:
She is intrigued by the rumors of Eothas' manifestation, but she fears what that will mean for her fellow expatriates, many of whom followed his previous incarnation into war and defeat.
Her conflicted views on his return might be sufficient to remove any requirement to defend Eothas to the death, or even to leave the party depending on how you deal with her and/or things develop throughout the game.
Which assumes I am not planning a great deicide for the reason of thou shalt have no gods. Although if he is a somewhat of a good guy after all starting with him might be problematic as I’d remove the force that stands in the way of divine maniacs (besides the usual fact that killing a good guy is problematic). Removing them from positions of power without killing might be an option as well, but I’m not sure how it should be done. Or maybe some killed, some removed from power.
It's less that I assumed anything about your priestess of Eothas (and I'm not sure why you'd bother to spoiler that) and more that, in my preceding discussion of options focused on killing Eothas, I hadn't considered how that would play out for Eothasian Watchers at all. But sure, I've no doubt players can find reasons for potentially wanting Eothas dead despite still technically being priests of his faith. I'd hope that the game reacts to that, even if I personally have no intention of playing an Eothasian Watcher any time soon.
That said, I suspect that Tagaziel's right in that the game is unlikely to portray a deicidal route as being particularly reasonable; at the very least, I'd be surprised if the game didn't devote a significant amount of time to considering the potentially disastrous consequences of killing Eothas.