Seriously though, don't go the passive aggressive route. As a manager, that always pisses me off. A good leader can and should accept legitimate constructive criticism and consider all of the angles. Honesty, your own position kind of comes last in line. What is best for the kids comes first (that includes the new set of students), then likely the whims of their parents, then your own personal concerns (assuming she can leave hre own ego out of it). School operations are in there somewhere too, probably ahead of the parents.
But you do have some valid points that should be considered. Present it as what you consider best for the kids and best for the school. If she insists on the new way, ask for some feedback and clarification.