I think what's missing here is that while apple may or may not ever prevent third party apps using third party distribution methods, non-app store apps may be depreciated- officially or unofficially. Even in the most positive of lights, with apple using the app store to more tightly control apps and their installation, they will likely be able to implement features that only apply to app store apps, making app store apps more attractive.
Also, while power users may always be aware of the benefits of non-regulated, non-app store apps, the average user would likely gravitate towards the app store thus making it difficult financially for non-app store apps to compete.
In the end, I believe that if the app store is the success that apple wants it to be, it would benefit the average user to the detriment of the power user. But then again, that's the way its been for a while (and it does make sense for apple). However much we (the macrumors minority) complain that what apple does isn't necessary the best thing to do, the things that apple does do helps apple sell to the more general public. (e.g. selling a relatively feature limited iPad upset some of us who thought it could do a lot more than be a bigger iPod, but apple probably sold a lot more iPads because it was as simple as it was).
