Probably not what you want to hear, but from a brief experience I had, don't try to coach your wife or do any kind of programming or anything for her. Your wife is an adult too, and I assume she can read, so if she's interested enough give her your copy of the book and let her learn on her own (or help her find a coach / the many resources on this website). You can't force it on her anymore than you can force it on a random member of society. We all want the best for our spouses, friends, and families, but at the end of the day you can only control yourself. And when someone says "Well, I'll do it if you teach me, but I only want to do this one part" then they are not taking on the ownership, accountability, or responsibility required for a long term thing like strength training.
Regarding your actual question though, if she's not willing to learn the squat then you're not left with much. You can see if she'll front squat or high bar squat, but those are not in then novice program for a reason. Oddly enough, The Press is actually the thing that makes my back feel the best; one day it was stiff from squats and after pressing it felt brand new. Between that and The Deadlift she can get in a simple full body workout. Frankly though if The Squat bar position discomfort is too much for her to handle I can't imagine she'll enjoy The Deadlift start position much either.