Maybe there is a bug. You defeat her in combat and are then given the option to finish her off, or spare her life, and I think it's even possible to pursuade her to turn back to the light. If you did kill her the whole Acadamy should have gone hostile. If you let her live she allows you to leave peacefully.
On an aside, I actually just played through that part yesterday and thouht it was funny that even though I killed Uther letting Yashura take over, When I did find Dustil he didn't seem to be up on Uther's demise. He threatened to tell Uther on us and then attacked. I killed him which didn't make Carth happy. Is it possible to save him?