It's not all about "replacing", it's about getting him more involved in the rotation. When you start consistently seeing quarterbacks sit back there with all day to pick apart the defense, you have to change something up. Getting your best pass rusher on the field more seems like an obvious change for the better.
Also, I feel like the Iowa coaches know what they have in AJ and are going to unleash him during Penn State. Against an offense with the athletes like they have, you need to get your best athletes on the opposite side of the field to stop them.