But how do you resolve the impact of "equal protection" in the context of those individuals the founding fathers did not consider fully "persons" (such as native americans)?

This one is so easy degs. Even back then not all founding fathers didn't consider some individuals not fully "persons"

There were men who thought that black people were included in the definition of "persons" but had to compromise in order to move on. They figured these generous fundamental ideas would prosper.

As a matter of fact what was in many founding fathers' minds can be found in their other writing. Because Scalia's problem is that he seems unable to actually get it right what these founding fathers were thinking doesn't mean it can't be done.