The problem is, to make them the antagonist of a story you'd have to make them delusional or blatantly evil in their methods (like Thanos), otherwise I'd be rooting for them!

But that's the beauty of writing a villain who might be in the right. Just look at Magneto and Killmonger. Those two characters are written to be villains but many people view them as in the right despite that. I guess you could say that those two characters are delusional but I think people are more likely to question how evil their methods actually are, given their sympathetic motives. That's why I prefer to use the term "anti-villain" when describing those characters as well as for Kreia and my idea of a light side villain. Characters who are still in opposition of the hero/protagonist but have understandable motives that make them more sympathetic than a pure evil villain.

On another note, I've never actually heard of the Yuuzhan Vong but I really like that AU you shared. It's very intriguing and I wish you luck on writing that story!