You defend him the same way you defend all "dual threat" quarterbacks... you force him to stay in the pocket, read defenses, go through his progressions, and beat you being a pocket passer.
You force him to beat you with his decision making.... force him to make good decision, after good decision, after good decision... Make accurate throw after accurate throw into tight coverage.
You don't rush him with your ends like you do a typical pocket passer... you try to keep contain on him and force him to operate from the pocket.
Rush 3 and drop 8 into coverage if you have to... make him find the holes in zone coverage or check it down.
If he can beat you that way then he just beats you.... but it's a lot harder than they think. Which is why pocket passers are one's playing in superbowls every year and winning Lombardi Trophies.