Ria, I think it was an unusual situation with my mum in that although I wouldn't have guessed, I also wasn't surprised, it was kind of a case of "ok, what's she going to do next" and she "came out" when I was 19, so I really wasn't bothered about it. Also, I don't think about the physical implications of it as really no-one wants to think about their parents having sex gay or straight!
But as for you and your friend. Firstly it's difficult to be objective about anything when you are pg isn't it! I probably wouldn't use your feelings at the moment as any kind of barometer of how you really feel!
Secondly, I don't think it is unusual to feel a bit funny about it. I am sure you are not homophobic, it just adds a new dynamic to your relationship. I guess you have to think about what it is that makes you feel funny. Are you worried that she might come onto you (which is a common but usually unfounded worry)? Or is it that she has changed her lifestyle, and it's not fitting into the perfect picture that most of us imagine? I don't know. But it's pretty normal, and how you deal with it would depend on the type of relationship you have with her. She obviously trusts you to have told, and you don't want to upset her by saying something that might offend her. On the other hand (and this is exactly the sort of thing my mum would say) if you are feeling funny about it for whatever reason it will be "out there" and she will probably pick up on it, so some times it's better to deal with any issues and you will probably feel better by discussing them and understanding her choices better.
Sorry you probably didn't want a session of psychoanalysis - and really, I don't have any answers just my own experience and my psychology MSc which qualifies me for nothing!! But if you need to talk about it some more I am happy to!