Let's play this out: you're assuming that side-loading would occur IN ADDITION TO distribution in the App Store. If Apple allowed side loading, then many of the large developers, who can afford the cost of services and compel their user base, would require that their apps be side loaded. (If Facebook removed WhatsApp and Instagram from the App Store and required sidleoading, all of their users would do just that.) That would essentially remove the largest revenue resource from the App Store. As a result, Apple could chose to limit development of the App Store and run it is a loss-leader. Or start charging smaller developers a fee to support the App Store, again, thereby reducing the number of free apps in the App Store for consumers.
But beyond that, if popular apps were removed from the App Store, then there would be less reason for users to visit the App Store. Thereby further hurting smaller developers who would be subsidizing the App Store directly. The iOS App Store would have all of the same problems as the Mac App Store and Windows App Marketplace.
Smaller developers significantly benefit from the current App Store model because much of the cost is subsidized by larger developers. Also, there is marketing advantage to have the App Store include all apps. For example, a photo editing app that is in the top 10 on the App Store is significant only if the same ranking includes Adobe Photoshop!