There are two things going on. First, any new activity is going to stress the body more than something it's used to. I've seen weight lifters think they're going kayaking for six or seven hours, only to come back after twenty minutes, unable to move their arms.

Second, and more importantly, her bike isn't set up right for her. It sounds like you got the saddle height right. What about its position front to back? Are the bars the right height? The right distance away? Bike fitting is a complicated art. Try the Sheldon Brown link for starters. If that doesn't work, post some photos here and people will critique her fit and posture.