That's pretty much it. I believe she thought that sacrificing the whole Jedi order (barring herself) was a fair price to pay (and in her own eyes the only way) in exchange for rooting out the source of the threat. But I didn't think she was evil. Just confused and deluded.
Nah. You only say that because Atris is exactly the complete opposite of Exar Kun. Unpredictable, with a deep, complex and credible personality, an interesting background, and most importantly, not relying on Sith crap to grant her uber 1337 powers of d00m.
The only thing I didn't like about her part of the plot was how the whole issue was resolved in the LS path. It just doesn't make sense to just leave her there to her fate (perhaps even allowing her to fall further) if your PC has been seeking redemption the whole game.
She should have had a hand in the endgame, perhaps dying in a blaze of glory, saving the PC's ass somehow, or whatever. Lots of dramatic potential wasted there. Otherwise, her subplot was one of the strong points of the game, IMO.