If I as the player find her to be evil, then she is evil.
lol, sry this just reminded me of the anakin quote from episode three
i actually dont think i disagree with your overall sentiment - i just think that alignment should be a working function of a bg3 game based on 5e. if larian includes/improves it where it impacts the gameplay in a meaningful way that, as you said doesnt set up biased roadblocks within the game preventing you from treating SH as evil, i think it will be real successful - i just want to see it first.
Alignment has virtually no rules in 5th edition. It is barely a thing at all. There are no spells or abilities that have anything to do with alignment, and there are a tiny handful of legendary items that can change your alignment. Outside of those, alignment has been functionally removed from D&D.
Now it is more a feature of the lore than anything else.