IMO they should have done what Geocaching.com did: limit the third party API to premium users. That way they would boost Reddit premium and app developers wouldn't have to deal with payment themselves. They could simply warn users that the app will only work when they use Reddit premium and that's it.
I am aware that this would still mean many users wouldn't be able to use third party apps, but it would be better than what they propose currently and it would also seem more fair (IMO).
It would also not necessarily kill commercial reddit apps. There are paid Geocaching apps around, that still need you to be a premium Geocaching user. And they somehow seem to survive.
Again: I would prefer it stays the way it is, but if they want to charge, then better just charge the user directly instead of fanning out the problem to EVERYONE.
z2k_