You can actually delete prototypes, but the way to do it is a bit arcane.
When you create a prototype component, mechanically what happens is a research project is completed that activates the prototype. This means that you can remove a prototype component by going into the Research window, filtering by Completed projects (radio button in the bottom-right corner), finding the prototype component in the list of completed projects for the associated field, and using the Delete Research button.
Having a button for this in the class design and/or tech summary window(s) would be way more convenient though.