I trained through back pain on my first LP. I started squatting literally nothing and it was very scary to learn how to train through pain. That plus being in a gym environment with my strong brother and big doods made me feel kind of lost. Could I get strong like them, did I want to, how do women do that, were all nagging questions, despite knowing empirically that I wasn't going to get big or veiny or mannish.
The Starting Strength women's group on Facebook, Bar Belles, was and continues to be a great resource for encouragement and inspiration. We post about many many different training issues and often feature our 60 year old moms and other older female lifters. If your wife is on Facebook, she should absolutely join, and if she isn't this would be a great reason to get an account. Seeing other people - other women! - who share your values and goals is so so helpful, especially when things get tough or scary.
I would have her pull if at all possible. For myself (which could be totally different than your wife of course) the squat continues to sometimes exacerbate pain if I allow myself to be too mobile, which is a very common problem for women. Have her keep track of how she feels before and after, and she'll see the difference in her pain right away. That plus having some role models and cheerleaders online in an all-female space should keep her committed and motivated.
And for the love of god, shell out for some microplates! My mom (62 years old, no athletic background) makes 0.5# jumps on her squat and just recently stopped squatting to a box and is still reaping huge benefits from lifting. Your wife doesn't have to go HAM to start feeling and moving better.