More than that, I think this will result in Apple being a bit less laissez faire about what companies do with their certificates. I think they may even look to change the system, maybe make it so that enterprise certificates have to register the devices they are installed on.
I expect in future you'll need to push these apps to the official app store, but have the ability to restrict who downloads them (to registered devices, or accounts - like with the Play Store beta program).
This might open the floodgates for Apple to shut down even more certs.