Your wife can go through queues with the rest of the group, and simply tell each cast member that she will need to exit before riding. There's always an exit right before boarding. I wouldn't say that the queues for rides such as Star Tours, Tower of Terror, and Expedition Everest are as good as the rides, but they are worth seeing. When I was pregnant last time, I was nervous about meeting up with my husband and son after they went on a ride if I went on a different ride, so I usually waited with them, but that was my personal anxiety.
The Pangani Forest trail in AK is a good idea for while you are on the Safari (since that is long once you're on the ride), and Maharajah Jungle trail will work if she doesn't wait in line for Expedition Everest.
Hollywood Studios has several shows with seating -- you'd just need to arrange meeting times/places afterwards.
Test Track and Mission Space have interesting post-ride areas that would be easy to wait in.
In Magic Kingdom, when I didn't wait in lines for Splash, Space, and Big Thunder Mountains, I just people-watched. That was also a good time to go find a beverage to keep me hydrated (and less likely to have foot swelling).