Personally, my theory about why people thought the story would take that turn actually starts outside of the game rather than inside of it.
JRPGs are branded with that 'team up with your friends and kill God' cliche for a reason; it really does happen A LOT. I assume it's because in a game with a grand setting that nonetheless primarily provides violence as a means of interaction, people started wanting to enact violence against the biggest thing in the setting, which tended to be 'the analog for God'. Then eventually developers started indulging that, and things snowballed.
I don't think, deep down, people actually wanted to fight Hydaelyn because they thought she was evil; I think people expected to fight her, because at this point in the genre that's just the done thing, and were looking for a justification. Then Shadowbringers rolls around with a theme of 'light is not always good and sometimes has to be fought', and a pretty genocidal sadboy to say bad things about her, and bam, suddenly the justification has crystallized: that we'll fight Hydaelyn because she's evil. The fact we'll fight her was never really the part in question, it was just a matter of finding the path they had to backtrack down to explain why.
I know I expected we'd throw down with Hydaelyn, I just never bought into the 'because she's bad' explanation, and landed on something closer to what actually happened, that we'd have to fight her as part of some kind of rueful challenge that we'd ultimately feel sad about.