I know that you're the good guys and that you're supposed to not be savages but at best she's a war criminal and at worst she's a maniac who killed hundreds of people for her own gain, the empire would have you in the chopping block for the exact same reasons (the wol stands atop of a mountain of corpses), so why are they dancing so much about this?
There's only two outcomes, one she gets thrown into a prison cell for the rest of her life, or two she gets killed, anything else and its bordering in stupidity even if the Scions/Lyse/WoL are good people.
Pretty sure the DRK quest is all about how justice demands no less.