That's one of the thoughts that's crossed my mind, but not just in regard to Apple stores; it almost smells like they're looking to ultimately take complete control over all software that installs on a Mac.
I don't think that's Apple's goal, and I don't think it'd be possible even if it were. There's nothing to prevent anyone who doesn't like the App Store from getting software from other sources--and in any event, the App Store model really isn't appropriate for a lot of software (think Microsoft Office or Adobe Creative Suite).
Apple can lock down consumer electronic devices like iPhones, but they can't lock down full-fledged computers. Nor would they want to; a thriving software ecosystem is the thing that keeps the operating system relevant.
