Sister Wanda is just a victim of the church culture. We have seen she's not actually evil, but she's still dealing out inappropriate punishments that do more harm than good. Such things happen when over the centuries an organisation petrifies. Rules are being followed with nobody questioning them, simply because they have "always" been there, so they must be correct. They tend to become more severe over time because when you grow up knowing nothing but the life under such rules, they don't feel as tough anymore. Generations of trainees are treated in certain ways, and in turn those of the trainees that become instructors themselves continue the tradition, without giving it a second thought. It would take an outside force/perspective to change it all.