After thinking about this for a while, if Haley's mom knew about what happened with Mr Klaus (since she put a stop to it), why is he still teaching, and why is he not in jail? You'd think he wouldn't be allowed near kids or anything. So why was there no apparent punishment for Klaus?
We don't have witness to what happened between Haley and her mom, but we do know how she reacted when the MC found out. Haley claimed complete responsibility and asked him to forget about it. Even claimed that he was being 'just like Mom'.
So, I can envision a scene where Mom doesn't actually catch them in the act, but finds physical evidence while changing Haley's sheets and confronts her. Haley has been intimidated and bullied by an authority figure, and feels guilty about reacting positively to the sex itself. Don't forget the blackmail aspect either. He has called her a slut, and threatened to spread that all over.
So, Haley claims to her mother that it was all her fault, and pleads that she doesn't want Klaus punished. Mom reluctantly agrees, and only stops the tutoring. I suspect that Haley also persuades Mom not to tell Dad, and certainly not the MC. However, from that day forward Mom no longer trusts Haley's judgment, which is evident in how Mom acts towards Haley, and in several conversations she has with the MC.
Was that the right thing for Mom to do? No. Should she have had Klaus's ass at least fired? Yes. [Prosecution of Klaus would have been difficult, however, with Haley being a poor witness in court.] It might not be a terrific rationale in real life, but I think it works well enough for a porn game. And in real life, I've heard of a lot worse rationales for people not coming forward in abuse cases.