Sometimes I wonder: how can a single person fap on something that he/she likes? I mean.. right now I'm reading the scans of AOT and.. I seriously can't read doujin like this while reading the original manga, even if these are based on my favorite ship.
Same thing for the other one about Tsunade and Naruto. I've finished already seeing the anime and reading the manga, but.. I simply can't, somehow XD
It is kind of strange, and it does make me feel guilty at times, oddly. I guess that characters that I like feel more human to me, and thus more interesting! I feel bad if I let myself think to much about, for example, the number of Evangelion rape/bondage/whatnot doujin or hentai I've masturbated to, but I mostly put that off by compartmentalizing my lechery and keeping it basically separate from the part of my mind that is able to empathize with the characters in question, and the part of my mind that has morality.
That's my basic answer - don't think about it, and compartmentalize. Don't think, for example, about what a horrible, awful thing rape is, or how it creates wounds that can never fully heal - instead, just keep enjoying watching a group of thugs running train on Asuka or whatever.