Eh, the answer is pretty simple. Crush the decision-maker. Not only does that intimidate him, but really, you just need to use one player (the backside DE) to take out the QB. usually the way the zone-read option works is that you leave the backside DE unblocked, allow the play to flow to one side, and then the QB can pull the ball and run against the flow. If you just have that DE take the QB out every time he runs it, you have one less guy to stop the run but you've also eliminated the optin part from it.
Now, the idea of teams using their QBs more as runners is one that would certainly be difficult for teams to stop, as the offensive team will finally be using all 11 players in the run game. Only problem is then you are opening your QB up to injury and I don't know how many good dual-threat QBs are in the league.