I've talked a bit here (https://neospring.org/+r/0e43226377) about Isabelle learning about Cy's past actions, and how she weighs it morally, but since you compare it to Alec's actions I'm going to talk about how she feels about that!

For Isabelle, a large part of the horror of Alec's actions came from the violence, the way he robbed her of control and agency, the brainwashing, the cruelty to others...all this extreme, intensive, horrific stuff that Cy just never enacted on his students. Isabelle doesn't think that what he did to his students was okay, but because it wasn't violent, she can't really bring herself to care (love reminding people that Isabelle is not really a good person) especially because it was in the past, so while she finds it upsetting at first she ultimately lets it go.