All these problems could be solved if there were a way for companies to transfer your existing non-App-store licenses to the App Store, allow for paid upgrades on the App Store, and allow App Store licenses to be associated with real serial numbers (or something else) that could be used to "take" your license with you, in the event the App Store suddenly becomes too restrictive.
Basically make it seamless, monetarily and "upgradily", to go to/from the app store.
That would be a good start, although a significant expansion in the available sandbox entitlements would also very likely be needed for developers who have already fled to go back to the store.
Well I imagine you'd only ever need to move to the App Store because of an upgrade which required it (because certain features are only available to App Store-distributed applications). So Apple would get their cut of the upgrade fee, and future upgrade fees as well. Obviously it's not as much as the full app immediately, but ideally over time it would add up for them with paid upgrades.
Basically make it seamless, monetarily and "upgradily", to go to/from the app store.
Of course, Apple will never let this happen.