it sounds obvious but the key against any sort of option football is to just be disciplined and not make mistakes. when an option offense is rolling, it is almost impossible for the defense to stop them from getting about 4 or 5 yards per play. but, if the defense limits mistakes and remains disciplined, it is very difficult for the offense to make the correct decision on the ~20 plays in a row it would take to score when averaging 4-5 yards a play; it's why you almost never see 15+ play scoring drives.
the answer is to rep it in practice over and over again to limit the amount of times the defense makes mistakes. the good thing about the quarterbacks you mentioned is that they play for penn state and michigan, two teams who we are more talented than. when you're the more talented team, better players can make big plays at a higher rate which can knock the offense off schedule, which essentially removes the quarterback run threat. being more talented also helps mask mistakes, because more explosive players can make up space quicker if they or a teammate messes up. we saw this plan work in several drives against nebraska, where we did not allow any big plays and eventually forced a mistake in the form of a fumble.
there are other tactics which can work, like on standard downs (i.e. not obvious passing situations like 3rd and long) we may blitz a linebacker and tell them to only go for the running back (called "blitzing the back") so that if the QB hands the ball off it's an easy tackle for loss, and if he keeps it we will be prepared because the play was specifically called to force a QB run. tactics aren't strategies, though, so this isn't a call you can make all the time because the offense can easily scheme around it but it's a good mix up from the base defense.
unfortunately there isn't one easy solution and the best way to counter it is "be better than them and don't make mistakes, they'll make one eventually". can we do that? absolutely. do i trust borland, browning, and proctor to consistently execute at the highest level? not sure yet.