Hime, what is your source material that your fanfic is based on? I'm sure you can post a book or movie title here without retribution- my interest from reading your inner debate is piqued. As far as being bothered by your fantasies, I think that you should go easy on yourself. Particularly when just writing a story (not to diminish its significance or anything). I myself have a couple of very violent fantasies that I would be greatly disturbed by should they ever actually happen in R/L, to me or anyone else. The point of it all is for them remain in fantasyland, where it's safe to explore what-ifs and inklings of desires without any consequences. Writing is the perfect way to "live" out these fantasies, so I think you should go for it in your writing! Good luck,
-Phan, her wheels turning