I built my LHT up from a frame, so I never had the stock cantis, but instead I started with V-brakes. They were fine. I don't know if the change will help your wife. Braking for over an hour sounds painful no matter what the brake is, so I doubt it's a question of brake style so much as hand position. And it sounds like you know what bar/lever combination can be used without causing problems. I'd go straight to that.

In terms of stopping power, I felt like switching to some Kool Stop pads were a huge improvement over whatever generic pads came with my brakes. Problem is, even with Kool Stop pads, you have to squeeze brake levers to stop, and you have to keep squeezing if you want to maintain slow, downhill speeds. If your bar/lever set-up leaves you uncomfortable, better stopping power won't help. It will just help you descend even slower so that you have to hold that position even longer.