I don't know if you've bought the mrs a new bike yet but I wanted to offer my 2 cents since I am in a very similar situation. I am female and have serious lower back problems. I ride a Sportster and when I get to around 200 miles the pain is pretty bad. I am 5'3" so a Road King simply is not an option. You've already gotten plenty of advice about how lowering the bike is going to compromise the benefit of a smoother ride. There are a couple of other things to consider for her.
1st thing is that, even if she can reach the ground on a bike like the Heritage softtail, if she has a really bad back like mine, she needs to be able to reach the ground and then some. The lower the better. When you don't have a bad back, you don't realize how easy it is to tweak it when you lean the bike over a bit and have to catch it with your leg, or when picking it up. If you think it likely that she'll trade out the Harley seat for something cushier, then she'll lose even more reach to the ground.
The position of the seat and handlebars makes a huge difference. I've tried out the Deluxe and the seat sits way too far back for me to use it at all, plus the handlebars would have to be changed. Those are some moderately high priced items to get to before all the more typical upgrades. The bike that works the best for me, without really needing any modifications at all, is the Fat Boy Lo. It is so low that I am very comfortable picking the bike up without needing to put my back into it. The seat is scooped pretty low, giving it kindof a natural low back rest, and it sits far enough forward that it's comfortable. The handlebars are positioned pretty well.
Weight really does make a difference for us ladies given that we lack the muscle mass and height that the guys take for granted. Since Harleys are heavy no matter what way you go, center of gravity is crucial. I think the Fat Boy Lo is the best I've come across so far. However, if she doesn't like the styling of it, the Deluxe could work with some modifications. It feels heavier picking it up than the Fat Boy Lo, but she's got a couple inches on me so that might make the difference.
I hope this helps!