It felt to me a lot more like a freeze response. Think of it as an alternative to the more well-known fight-or-flight response. When sensing danger, your body freezes up and you can't act. In this case, even if normally Katherine would have been able to fight back, she would still have been unable to physically stop the protagonist. A lot of real-life rape happens like this.
The protagonist rationalizes that, since Katherine was able to fight off that guy in the alley, it surely must mean she could have fought her off when she touched her, so her consent is assumed. However, a person can have different responses to different people, especially when you consider that the protagonist is someone who Katherine has some deep-seated emotions for. So it does feel very much like rape to me.
If you're having sex with someone and they tell you to stop, even if they don't physically try to stop you, you stop.
While this is an interesting comment and i agree, IRL you are completely on the money, however this is BM, none of the characters, save perhaps CJ and Hannah are even remotely normal, Katie has specific history with the MC, it may not seem consensual but trust me, she is just as keen as Ellie or Jada, i suspect she would even see it as romantic to a degree, though she'd never admit to it.
Yes, the MC does rationalise it and that isn't exactly a good sign for the MC's mental stability but you need to remember most of the main cast are broken birds, that in a lot of ways is the point of the game, trying to unpick the trauma and work out how it will come good.
Is it rape, IRL of course it is, in game, no. It seems like it at the time to the player, it seems like it to the MC but i very much doubt Katherine saw it that way, she's been thinking about the MC in a heroic light for some time now, she is distant with her BF, she has issues with intimacy and frankly i doubt she's ever been the initiator for sex at all, if she has even had sex before, it wouldn't surprise me at all if she didn't have the largest baggage aside from Ellie in the game, psychologists, what can i say.
What i'm getting at is i highly doubt she'd know what to do with conventional advances let alone molestation, now add in the fact that she actually likes the person molesting her, she's going to go along with it.
Now the only way to be certain is to have it from the horses mouth and see what Recy says, but the guessing is half the fun with Katie.