I agree that a proper apology to the MC was necessary, but not that only the MC should end up alone if the friendship path is chosen.
All 3 of them have feelings for each other and M&J had just gone through the most tumultuous time whereby they each developed feelings for a guy, which was especially significant in Maya's case. Why then M&J just forgive, forget, and get back together so easily is baffling and, as I've said many time before, a better solution would have been that they all remain friends with none of them being in any kind of formal relationship with the other so they can have time to figure things out.
This is what should have been the automatic option on the DIK path where instead of being flat-out rejected for reasons that seem completely nonsensical, they would all essentially "take a break" from each other to figure things out and be allowed to try and repair the damage with individual scenes where the MC, and the player, could get a better sense of what these girls are and were going through and why they did what they did.