Eric, I work the epoxy vigorously all over the hull, staples and all, to make sure all joints are filled. My experience is that the cured epoxy protects the wooden surface from denting when pulling the staples. I use a Rapid (Swedish brand name - do not know what it may be called elsewhere) staple remover that has two yaws securing the staple and a large bottom plate to use as a lever. A few staples will pull fragments of wood, but these are normally shallow and more easily sanded than the dents from pulling staples in non-treated wood.

Bjorn