What is the best way to charge a customer a pro-rated amount on a product when using the 'Add an Order' interface?

My client offers yoga classes on a commerce kickstart install and once a class has already started, they want to be able to charge the client slightly less than the normal rate, to reflect them starting late. However, when the site owners use the 'Add an Order' page, choose a product and then manually reduce the price amount, the order still charges the full amount. Essentially, their change is being ignored when the checkout pricing rules are triggered.

Should we be using a different method to implement a reduced rate on a product? Perhaps using discounts? Any help would be greatly appreciated. Thanks.