Well, whether or not Flora gets raped by the tree depends on your actions, but she was blinded at the time so she didn't even know it was a tree that attacked her. There are follow up quests to the tree though where she's against entering the forest due to the attack, and she does talk about the attack if you help the tree have its way with her so I wouldn't exactly say she doesn't give a damn about it.
As for Kate kidnapping Isabelle, I mean, it was a one day thing and not even overnight so who would even know she was gone? The classes are self serve so the students can choose to go or not go (and of the three classes she chose, only one of them has a teacher. Well, teacher's assistant anyways). She got roofied, broken in the evening, returned home before night, so to anyone not there, it'd seem like she went to school and came home. And Kate even mention that she cooked up a house party alibi before this in case Isabelle went to the cops. Might be some other details that I'm missing too, I only did that route once to unlock stuff. That route isn't my cup of tea and definitely not what I would choose naturally.