Wow, just had this conversation today with my friend re: The Mortal Instruments.
*spoiler alert*
Two of the main MCs meet, fall in love and then find out they are sister and brother. However, they couldn't get over their feelings for each other and there was all this weird crazy tension between them because they wanted each other, but knew it was immorally wrong to feel that way. Well, needless to say, I wasn't buying they were actually brother and sister because they do end up kissing and having a really hard time not wanting each other, so I quickly realized that the author must have been planning to remedy the situation because I wasn't buying that she would allow what happened to happen if they were REALLY brother and sister. So, the relationship between them and how they wanted each other even though we were supposed to believe they were siblings never affected me. I always believed that in the end, we would learn that they actually aren't brother and sister...and I was right

.
Now, my friend who loved the story (for the most part) was deeply disturbed by this story line. Even though at some point she suspected they might not be brother and sister, she thought the mere idea of these two characters wanting each other while believing they were brother and sister was disgusting. Actually, she used the word "disturbing." It really, really bothered her. Yet it didn't bother me at all. Maybe because I don't have brothers (she has 2) or I was able to convince myself early on that there is no way this Cassandra Clare (the author) would have true incest going on in her book, I was able to see past it and actually root for this couple to be together.
So, I guess it will be different for each reader and what their own experiences, beliefs and preferences are, but isn't it like that with pretty much any novel? I say write it and don't look back. Tell your story.
Mel