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.