But I just feel hurt by how she’s doing this.

Then imagine how she must be feeling. Not only are her hormones all over the place, but this is one of the biggest things that is going to happen in her life. She should be feeling so happy right now and yet her best friend, one of the few people who she'd expect to be there for her through everything, is avoiding her and not supporting her and tainting the whole experience for her (when, like you said, she supported you through a lot of stuff).

All because "vomiting and pregnant women freak you out"

And she's right. Babies get sick. Does that mean you're just going ignore he babies existence too? Are you never going to hold her child in case its sick on you (because trust me, it happens quite a lot). You're being childish and selfish.

If you want to salvage your friendship, you need to apologize to her and see a therapist to deal with your issues (or if you don't want to see a therapist, you're going to have to confront them by yourself). Asking forgiveness isn't wrong (I'd say it's actually the decent thing to do) but only do it if you actually intend to make an effort to change because if you don't then it's completely pointless.

This might seem harsh, but this isn't coming from someone who just doesn't get it -- I have an anxiety disorder and have bad panic attacks with specific triggers but I've never let that stop me from being there for friends and family.