Yes, they can still do their own payment processing. Again, what you seem to be misunderstanding, is that the problem is not IAP, it's not being able to manage your own outside the App.
It's the fact that IAP is not optional anymore, especially if you offer subscription or payments outside of iTunes.
Please, wrap your head around this. IAP is not optional. It's either you don't offer DLC/subscriptions or you have to implement IAP side by side with any kind of payment processing you already have.
Even worse, you say you just have to make your own solution more compelling than the IAP. That's kind of hard when Apple will reject your App for including links to your site or any kind of information trying to convince users not to use the IAP.
Again, the simplest solution to this for Apple is to make IAP completely optional, like it used to be before all these rules came to light. If it is, no one will care how much Apple charges for the service since no one will be forced to use it.