To be fair, KOTOR2 lets you roleplay a traditionally virtuous Jedi, who insightfully points out Kreia's hypocrisies, fallacies, and motivated reasoning, helps others out of compassion, and vindicates the values of the Jedi, even as its individual members miss the mark.
You can engage and agree with the deconstruction, or you can tell Grandma Avellone to fuck off. I respect that.
At the end of the day, Kreia's the villain of a story about a broken galaxy where everyone's desperate to find a purpose to justify their existence and ignore the greater threat looming in the sequel-that-will-never-happen, and your job, dark or light path, is to kick her ass.
The deconstruction of both Star Wars and RPGs in Kotor 2, even in it's unfinished state, works because it's filtered through in-universe sources (The normal RPG main character/companion dynamic comes from the Exile being a wound that's unintentionally influencing people, Kreia's philosophy is basically based upon taking 'May the force be with you' waaaay too seriously, the borderline worship of Revan comes from the cult of personality he built up). Rather than current day meta commentary where characters are talking in a way that only makes sense from an out-of-universe perspective (i.e Luke and Kylo literally telling Rey that she can't be important because she doesn't have a famous family name or Han mentioning how these super weapons always have weak points to exploit).
I also never saw Kotor 2 as supporting 'grey morality' or Jedi being worthless. It all surrounds how the effects of the Manadalorian Wars still echo to the present. It's not that the jedi are really the evil ones or that they have no place, it's just that Revan seemingly proved all their fears about their possible interference in the wars leading to the creation of something worse, that when they finally attempted to do something, they were immediately wiped out by their enemy, leaving the survivors too fearful to make any direct action or learn about their enemy.
It's not that the Jedi and Sith are the same, it's that the average people who don't give a shit about nuance and have nowhere near the power force-users have just see a civil war between jedi and jedi who wanted to add red to the lightsaber colours that they always seem to get caught in the crossfire of. A perception not helped by how all the living Sith you face in this part of the Old Republic era are all basically fallen jedi. Even Kreia's view of the Sith is that they're self-destructive fuckwits whose only use is to be the fire under the ass that gets the Jedi to realize they need to act.
Kreia doesn't really give a shit about your morality technically, she's happy as long as you display your decision process as more than 'This gets me good/bad boy points'. Which is why you'll actively lose influence with her if all you do is pick the options that seem to just blindly agree with her. She's like those annoying philosophy exams you get in school, she doesn't care about your answer as long as you explain why with at least three pretentious words thrown in per paragraph. I think Kreia's a blowhard who's coping with her existential crisis through Revan Simping, but she works as a character because the story treats her as a person rather than Avellone's personal mouth piece... Even if she is. Your enjoyment of the story doesn't hinge on you clapping at everything she says.