Thanks all for the advice and support. It helps a lot to hear your opinions and to get an idea of what you think is the best way to handle this. So, as an update: I am still struggling, but not considering dropping out any more. I would feel defeated and like a quitter if I just gave up. The social reality in the department is that many more people now know. I can tell who knows; interpersonally it is not too hard to pick up on. So yes, the rumors got around, as you all predicted. And of course, this is a painful realization. It still hangs over my head everyday when I walk into the building, and I even have occasional nightmares about it. That said, there is plenty that has improved, namely my personal acceptance piece of this and the extremity of my reactions. I am no longer fighting for the ideal that my colleagues would all be able to keep my secret, but neither am I thinking that this will kill my chance at success or be the absolute end of my career. The most I can do is to remind myself that I am innocent. The wariness of colleagues is annoying and sometimes hurtful, but deep down I do not "feel" like a sexual offender, and with that, I can (for the most part) rest easily at night.
Not that this really matters, RISINGSTAR, but you are interpretting this in a way that gives the girl more benefit of the doubt than she deserves. If you had seen her "evidence" you would have realized her claim had no basis in reality. It wasn't even close. Essentially her story was like "I went to a bar, and then I don't remember what happened." I was with her, she was not stumbling, blacked out, or showing any other signs of being too drunk to offer consent. Even her friends didn't believe her. She led me into her bedroom, holding my hand, while her friends were in the house with us. She never said "no" or "stop" and she never gave any non-verbal sign that she didn't want to have sex. I spent the night. The next day I woke up thinking nothing out of the ordinary happened. She had a boyfriend at the time. My theory is that she woke up, realized she did a shitty thing, and flipped the story around to make herself seem like a victim (and maybe she sincerely believed it, as a way to keep her ego from shattering). I really don't know her motive, but I know I was innocnent. So did the police. So did her friends. It was barely controversial. It wasn't even close to as bad as it now seems in the minds of my colleagues.