In my head canon the reason why the MC (over)reacts to the Josy-Maya relationship the way he does, is not exclusively that he feels betrayed, but also that it exposes a very unwelcome fact about
himself and the people around him. In the bathroom stall he even says something to the effect of "And tell her what? That we are all just cheaters here?". The MC is pretty young and - in my playthrough - his mind is all over the place. He does not know what he wants and so bounces from one crazy situation to the next in this over-the-top college environment he has suddenly been thrust into. It is possible that he
genuinly likes
both Maya and Josy, but he really hasn't had a quiet moment to reflect on his actions since he arrived at campus. When he discovers their relationship he is suddenly confronted with the fact that
he himself is a cheater and it also removes the girls from the pedestal every guy at first put girls on at that age, and brings them down to his level.
So yeah, if you assume the above to be true, his reaction does kiiiinda make sense in a neutral playthrough. Then again, I am a Dr.PinkCake apologist