There are a couple details in this story that seem to just go over my head.
The male refers to sex as being so painful to him that he is loath to repeat the experience. Even when I was a child and first read the story I realized that this was contrary to the human experience and confused me. It must be important somehow, the point is reiterated 2 or 3 times. If the girl was purposely making it painful for him the ship should have noticed, since it had already gone through all of this numerous times and should know how sex is done. In a story this short, items like this should not be present unless they are important to the story.
The male frees himself without any help. he actually caused the short that gives him an excuse to return to the control room weeks before he even met the girl, as he says that the short occurred over three week after he nicked the wire. The girl was only to be around for 3 weeks and it sounds like it happened after the second day that they are together. The girl never says anything to him about freeing himself and wouldn't be able to anyway since the ship would hear. Then after he has freed him self, she claims that she freed him and he acknowledges that she did.