I think a very simple fix to that solution is for the Witches to find out about the MC's bigger plan; and that he's holding Elyon's life and the fate of the kingdom with him. I'll expand on the routes I mentioned yesterday, just to give a better idea of what I meant. So instead of playing cat and mouse and who's blackmailing who, the sensible approach would be;
1) Blackmail route: MC blackmails the girls one by one, but unwilling to fall prey to him again and again, they confide with one another to take him down. MC by then has garnered enough trust with Elyon to have her wrapped around his fingers and partially reveals his plan to the witches and threatens her life, in exchange for their silence and continued abuse. Knowing the stakes now, the witches have no choice but to comply, while they plot to convince Elyon about the snake pretending to be her benefactor. MC must take this opportunity to corrupt the witches to the point where they can no longer resist him, or else he fails completely and they rise up and thwart his and Phobos's plans. (Basically, the 2nd half of the game is a time-management/resource-management thing, and you have to balance between the corruption of all the witches simultaneously, while still slowly convincing Elyon to give herself to you.) This is the Slave Route.
2) Anti-hero route: MC blackmails the girls, but was not willing to corrupt them completely. His established relationships with them, while initially for deception eventually gave way to empathy and some emotion. Out of guilt and contempt for Phobos, he reveals the truth to Witches and the risk of what might happen if Phobos finds out he snitched. In order to buy time for the Witches to try to topple Phobo's plan on its head, MC continues to play things out as per the status quo, to avoid suspicion. MC can still date the girls (But with Elyon still being the primary love interest) and since Phobos doesn't seem to pay much attention to what you do as long as the results are favorable, you use that blindness to your advantage and the MC becomes a double agent, spying on Phobos while also reporting back to him. Once they were ready, they reveal the truth of her power and lineage to Elyon, and harness her raw power to destroy Phobos in a Coup d'etat. MC finally gets to sleep with Elyon risk-free, and the witches (depending on your relationship with them) act as your side chicks. This is the Love route.
Just off the top of my head. Could obviously use quite a bit of polish, but I think would make a plausible approach to the multiple routes thing which would serve as a better narrative for the game.
