A few things to say here.
First, There are two main LIs in this VN plus several side girls. That's been very clear since the beginning. Both will have multiple endings, and there will also be several endings with neither of them. So the game is not forcing you to focus on "just two possibilities".
Second, the Mallory scene in CH3 that you mentioned is, in fact, avoidable. You're not forced into it. That scene requires that you have 6 or more "Trust" points with Mallory. You got that scene because of the choices you made. Basically, if you treat her completely platonically up until that point, you will not get that night visit scene. So it is not a forced scene and it really shouldn't be hard to avoid if you really dislike or distrust Mallory that much. I think if you don't hug her in CH2 and don't raise Mallory's access level in CH3, then that's probably enough for her to reconsider making her move on MC that night in CH3.
Third, as you may have guessed, the "helping with intimacy issues" thing is more or less a pretext. There is truth to it, sure, because of her traumatic experiences in foster care, but I think it's more so that Mallory is already very attracted to the MC by Chapter 3. However if you still do get that scene and you choose to turn her down at that point, you don't have to feel like a dick for it. Mallory will be embarrassed/disappointed as she leaves, but that is a realistic reaction. She took a big chance, but Alex didn't feel the same. She gets over it and there are no hard feelings. Besides, that scene is probably the safest time to reject Mallory if you plan to remain friendly with her on a Jaye playthrough. There are far worse ways to reject and/or hurt her later on but only if you go full asshole.
Fourth, #MALLORYBESTGIRL