My wife said she wanted to abort and hoped for a MC, it's painful to hear that stuff (and she was having second thoughts with it even being planned). Sorry...

First things first just make sure she continues counseling/therapy. As an aside, there may be some medication considered acceptable, with minor risk to fetal development.

For the logic side of things... PhD or Masters? I went for a PhD, and I can't think of a good time to have a kid even after. After you are working on career advancement. I've heard if you're going to have a kid, grad school is as a good of time as any. By the time you are trying to advance in your career you have figured out how to juggle the child and responsibilities. I mean by the time you have stability in a career these days you are probably in your mid to late thirties when risks for genetic and fertility issues creep up.

Ultimately she's in control, she took you opinion in advisement, and on the flip side she chose her path two. You can only help her, whatever she chooses. That doesn't mean there isn't consequences to your relationship down the road.