TJ, you may be able to minimize the problem with thinner huaraches. Mine are made of leather painted on the bottom with plastidip. They are only about 1mm thick. I don't run as well as barefot in them, I think I may be pushing off a little bit but they are thin enough to not make me pound heavily.
One other possibility might be that you have tension in your arch because you're trying to prevent the huarache from falling off your feet. Maybe they are too loose in the back, or you need to get used to the idea that they will not fall and relax your feet.