Ok, I'm a little suspicious at this point too... I'm really not sure what kind of advice to give but I'll try my best at the bottom. I just want to point out one thing first that I realized that maybe you or whoever else answers this thread can analyze.
I'm not sure I would believe what your boyfriend said because how could his roommate have had such a serious conversation about something like that (rape) with him considering how drunk she was? And also, why would he take her seriously about that if she's drunk and her sense of judgement is shot? I mean, I don't think anyone who goes around screaming "I want sex!" can be taken seriously...at that time, at least.
I'm not sure what to tell you. I know this seems to be the universal "thing to do" but I think you should sit him down and talk to him and demand the absolute truth, and give him reasons as to why you question what he told you. Also, let him know that you heard and saw him wink at her. If that had anything to do with what went on up in her room for 45 minutes then maybe he'll feel stuck and feel like there's no use in lying. (Of course, I'm not saying that he is lying.)
Just talk to him. I hope my advice helped a little.