I remained sympathetic towards her until the... colourful issue with Yo. Until then she'd just been doing evil out of survival instincts or devotion to Fuminori, but That Event was borne out of some inherent cruelty on her part. Fuminori was a dick from start to finish though. I'm still claiming his being a dick rubbed off on Saya.
Also also MM I know you hate anime etc etc but I have to recommend you read/play
Ever17: The Out of Infinity. It's the best vn I've ever played and I reckon you'll like it because it's
very sci-fi. Also contains time travel dickery.
If you do decide to give it a go though, wikipedia's Detailed Plot section will absolutely ruin it for you. So don't read that.
Also give it the benefit of the doubt (It's good, but not incredibly so) until the fifth route where it suddenly becomes one of the most intelligent science fiction stories I've ever read.
EDIT: Also the pseudosequel
Remember11: The Age of Infinity is nearly as good, and has the most brilliant late plot twist ever, but a much weaker ending.