It reflects Shinji's creativity and eclectic nature, in that he also abuses in ways that are not rape.
This is intriguing, though. My usual take on ZnT is that Saito deserved roughly 30-40% of the crap that Louise dishes out because he is a complete moron and pervert. I figure that with Shinji's greater capacity for genuine evil, that'll get that percentage up higher. Thus, the relationship will be a 50-50 balance of who's going to be the monster today! A much more likely scenario for long-term happiness. (Actually, the thought of two of the characters whose canon versions are among my most hated characters in Japanese media spending 500K words brutally abusing each other sounds very cathartic!
)