Agreed 100%. Not to mention the fact that Shiho's very comfortable talking about love/relationships in general, which I don't think would happen if she was raped.
I've always had the impression Shiho had plenty of 'power' (for lack of a better word) while in the Org, and wasn't as 'sheltered' as many would believe. She was young and already led an important research, and seemed to have knowledge/interest in many 'normal' things (fashion/relationships/etc.), which is rather interesting. We know she didn't see her sister much, then who gave her those kinds of knowledge? Vermouth? lol
Another thing that drives me further from those rape theories is the fact that Gin, so far, has been shown to be very hierarchy-savvy (see: his treatment of Vermouth and Bourbon). As he himself said, she was an indispensable member, and thus I imagine he wouldn't want to risk the boss's ire by doing something improper to her.