You pretty much just said it: rape is no small thing, it's very important, hence why the filmmakers backpedaled on it at the last minute. I guarantee that this isn't something I've made up to fit my narrative. If I can, I'll find and post the snippet that I saw but I assure you that was the original intention.
Jason coming at a knife can also be seen as an intimidation factor. Immediately, Chris kicks the knife away but it phases Jason not a bit and he continues after her. She recounts kicking and screaming and ultimately fainting, later awakening in her bed and her parents deciding not to speak on the incident.
That right there implies what they initially intended: rape. Sure, it doesn't fit Jason's character but that's what was written originally before they got cold feet. Again, that's the only reason she could possibly survive such an encounter when no one else has.
Chris was defenseless, fighting to the best of her ability to no success and then she faints and the last thing she remembers is being dragged off by a mongoloid. Even with the edits, the direction suggests said approach. Again, why else wouldn't her parents ever reference the incident? Finding your daughter in such a state isn't exactly an element you'd be willing to revisit.
Given Jason's history, method of execution and everything else, rape is really the only thing this situation can account for. He was alone with Chris, and even without a knife had the capability to murder her without second thought. Why didn't he? Because that wasn't his intention per the writers.