Equality is nice and all, but that's not how exercise or cycling works. As a person who is similar in both size and weight to your companion and only rides 650b, 650c, and 26" bikes, I don't expect to achieve the same amount of exercise as the person I ride with. It goes beyond wheel differences (ie physical differences, bike gearing). Wheel travel is also affected by rolling resistance. The difference in wheel revolutions are dependent on the gearing one is riding in, even if one covers more ground than the other. I'm not trying to argue with you, I'm simply stating facts.
If she's happy with the exercise she's getting, then who cares if she has to work harder? And if you're both comfortable, that sounds like a win for everybody.