I think what they will start doing is blitzing the merge point, and hitting the QB no matter what. Teams that use it a lot will need 2 QBs who can run it.
In order to even try to do that you would have to know exactly when the team is going to run the read option and what side it is being run to. That likely won't happen.
Also if you try to do that then the offensive coordinator will probably pull a guard and fullback to that side and just run power off tackle and shred the huge holes that will open up when the DE is over pursuing and leaves a gaping hole on that side leaving a running back running through a gaping hole with two lead blockers, Big run and likely TD city.
The third thing is the screen game and slant routes will blow that look up if you try to blitz constantly to take away the read option.