The iOS App Store does the same thing with changing the rules in the middle of the game, but it is not subject to potential irrelevance because it is the only place to get software for iOS devices. So the obvious solution for Apple is to make the Mac App Store the only place to get software for MacOS. I'm actually a little surprised this didn't happen in 10.8.
What Apple may do is stop developing MacOS altogether and make a variant of iOS for desktop after OSX (or simply rebrand). And I don't think this would be a total shock for the users by the time. Largely because Metro app would be following the store model too.