Okay thanks for your two replies. I was getting really frustrated, but I just figured out how to resolve it after reading your replies. It's kind of counter intuitive in how specific it is to rape someone. You have to (A) interact (meeting) someone, force them to have sex, then specifically subdue/hold them down, and then tie rope around them - that seems to be the only sequence of actions that lets you do any other sex actions.
Anyway problem resolved. I also just realized if you force them to have sex and they get into it, the rebelling thing goes away almost instantly. What a ****ing relief that is.