Most big box stores receive frozen meat, then thaw and resell. By refreezing completely thawed meat, you do risk some issues. However, if the meat is only partially thawed (i.e., there are still ice crystals and the exterior temp is no higher than 38 degrees) then it can safely be refrozen. The FDA guidelines note that meat held in the refrigerated can safely be refrozen.
I've never tried to apply a rub to frozen meat so I'm a bit hesitant that it would have time to help the meat "sweat" sufficiently to help the osmotic process between salt/sugar/spices and the cells of the meat. Beyond that, if you try to inject even partially frozen meat (like brisket) I don't think you'll see the caliber of absorption you're wanting.
As far as the rub acting during the thaw, I can't find any info saying it will or won't work ... but it might be an interesting (and potentially expensive) experiment. I'd be inclined to find a good local butcher who can verify that their meat is "fresh, never frozen", rub the meat and let it sit for at least 6-12 hours and then freeze.
An alternative, if you have a good vacuum sealer, is to pre-cook your meats and seal them for freezing. Having saved portions of pork butt, brisket, and even ribs I can say that they are very good (though not great) using this method with a reheat on the grill after they thaw.