That we know, all this is just a theory. However, considering that Marilyn confesses MC on the Chloe is Strange route that she made that spell at a time that is unavoidable in all possible routes of the game (when she took advantage of her psychic powers to enter in his mind during the morning of the Day 4), it is logical to think that the spell has also happened in the other two great routes of the game ("Chloe is still MC's girlfriend" and "Chloe is no longer MC's girlfriend") but MC wouldn't even know the spell existed nor would Marilyn suspect that it backfired and affected Chloe instead of Nicole.
If this theory is finally on target, I imagine that the spell on those routes will be discovered very soon when the normal medical methods to wake Chloe up don't work at all. Perhaps after that, Marilyn will have a hunch about what really happened and sneak into the Heavens' house to confirm her suspicions, at which point she will be caught by MC and will no longer be able to keep her dirty little secret to herself, having to confess to MC what she intended to do to him and Nicole. I imagine that this route will provoke a greater feeling of betrayal in MC, which could lead to a progressive distancing between MC and Marilyn, which would be even greater if during that game MC has few Marilyn relationship points.