I think it has to do with advertisers; the pages were scaring them off. This, I think, is a huge problem. Rape has been a storytelling element for as long as there have been stories to tell. Hence, discussion of it is very relevant to the site's purpose even if the subject is unsavory. On the other hand, you can sort of understand where the advertisers are coming from. I say "sort of" because, honestly, do these pages pose any threat to them? Are people going to say "I'm not going to buy that product, I saw that ad on a page that had to do with rape"? But no matter; advertisers do have the right to decide what pages they do and don't want their ads to appear on, however good or bad their reasons may be.
But, at the same time, it is very bad to have corporations essentially telling you what you can and can't talk about. Today it's talk about rape; tomorrow it could be something else. A site like TV Tropes needs ads to survive; a donation-based model might not be realistic, because the site is too big to be cheap but too small to get donations pouring in like Wikipedia does. So freedom of speech loses out.
I wish I had a solution to this situation, but I don't.