The Naruto series is about heroes, growth, and positive relationships. Introducing 'evil rapist' into a harem fanfic would not only be against the ethical norms but also against the essence of the Naruto world. It would damage the positive image of the characters and the overall feel of the series. Additionally, most fanfic communities have rules against such offensive content.
One major reason is that the Naruto franchise has a certain brand image to uphold. It is known for its action, adventure, and positive character interactions. A 'evil rapist' concept in a fanfic would be a stain on this image. Moreover, the fan base itself would not tolerate such content as they cherish the positive aspects of the Naruto story and characters, and they expect fanfics to enhance rather than defile the Naruto universe.