Aya knew. But she still had hope. Doesn’t mean she won’t put Sakuragawa down and then end her sensei’s life. She even explicitly gave him a chance.
One of the main things that separates the Medusa from the Dakini is not only experience, but their military mindset. The Dakini are a cult. The Medusa are a fighting unit. Religious fervour will only get you so far against disciplined teamwork.