But it sounds like her sister feels like my gf is abandoning her by having the baby

This struck a chord with me. I'm the oldest sibling of three, and for years, my sister (the middle child) was upset with me, but I had no idea why until she finally was willing to talk about it.

Turns out my sister was mad at me for abandoning her when I turned 18 and went off to college. I was like, what? That's a normal step for many people, it wasn't like I purposely left her behind... After we talked about it, she acknowledged that her feelings were irrational, but it bugged her that I got to do everything first and she was always feeling left behind. I could relate that this would suck, and told her I was sorry, and that I hadn't been trying to hurt her. She seemed to understand this, thankfully, but for whatever reason, needed me to acknowledge that it was hard to be in her spot.

End result, we are closer now than we have ever been (even though we live 1500 miles away from each other).

Your wife's sister might be feeling that same way, that she is upset she's not getting to experience having a baby first... maybe this is a pattern in their lives, or maybe it's just a bit of irrational thinking... or even mental illness.

Your wife will have to give her sister space... leave the door open if she wants, and hope she comes around and has an honest talk about what it is that's really eating her. They can't have a stable relationship until they get to the truth of the matter.

Anyway, best of luck!