@stilgar exactly, which is why she was pretty much literally the only suspect. Ray was told someone with power comparable to you has snuck into the school. The only one it could be aside from the teacher is one of the students, but like I mentioned in my previous comment, all the evidence pointed to the teacher. I think people just didn’t WANT to suspect her because she’s so likable. However, as an author, you either want the traitor to be an annoying villain, or someone the readers love, otherwise there would be no impact.
EDIT: That being said, she can still be a redeemed villain. Her tears show that she is internally struggling with what she is doing, and she even puts students to sleep instead of killing them. She also likely left Eugenics alone because she was doing a series of tests to verify Ray was the Iceblade magician, even though she had to reluctantly risk students’ lives. Author has the potential to make her into a deep villain with different views, but not necessarily evil. Possibly a survivor of the other side of the war that Ray had a huge hand in winning. So readers that love her, rest assured the author will probably keep her loveable, just with a different viewpoint. And no I don’t read ahead. I usually don’t like calling out foreshadowing because I don’t want to ruin readers’ experience, but I’ll make an exception this time. All of these signs were foreshadowed, you just have to read closely.