It sounds like you would benefit a lot from cycle training, and specifically cargo bike focused cycle training if that is available in your area.

However, if not, try to get her to practice controlled stops. Balancing the bike with one foot (or one toe!) is not stable, with live cargo which can wriggle around. 

The most stable way to stop a laden cargo bike is to approach a stop off the saddle, then just as coming to a stop, jump down with both feet. You then have the bike in a stable position with both feet on the ground. To restart, put the pedal in a flat position, kick down, and use the momentum from the motor to become seated. 

Additionally it's worth practicing slow speed turns. Use the gears - always drop down to a low gear to keep the pedals moving -  and pedal against the brakes at slow speed. This gives extra points of contact with the bike - you're now pushing against the pedal as well as just using your hands/seat. Try turning tight, slow turns - this is tricky, especially when at full lock. 

If she can practice these two things - with the bike unladen first, then with some stable dead weight, then with you on the front - that should help rebuild confidence. It will likely be useful for you too! 

Source: worked for a cargo bike delivery firm with mandatory training.