Just because Lion will be available via the app store does not mean it won't be on store shelves shortly after it is released. Nothing on Apple's site says one way or the other. I would suggest we all wait to pass judgement until we know for sure. It isn't available yet anyway.
That's what was announced at the Keynote, only via the app store. But I agree that Apple are no strangers to backtracking on their over-restrictive announcements.