You are correct, running into a loaded box every down isn’t the big-picture solution, but neither is dropping back to pass every down and abandoning the run altogether. There is a happy medium where you run it just enough for visual affect that they have to still honor the run, and that helps open up those vertical passes that will back them off. It's Chess, but Kelly treats it like it's checkers...when you abandon the run, the D pins their ears back for the pass and then your QB is constantly under duress and neither aspect of the offense gets in sync.
Sound familiar..?