At risk of raining on your parade a bit, the underlying complaint was from
Google, not Apple. ("This comes after multiple requests and threats by YouTube which ultimately led Apple to suddenly pulling the app from the App Store.") You're trying to make this all about Apple and the Walled Garden™, but the story as described by ProTube's author is rather more complicated than that. In an alternate universe where Apple let people sideload applications, the outcome isn't "ProTube 2 keeps being sold and everyone is happy," the outcome is "Google sues ProTube 2's creator into destitution."
And, you know, while I'd like to see Apple allow sideloading of signed apps (I think in the long run it's essential if they're serious about making iOS a general purpose computing platform), it's just a bit on the presumptuous side to assert that all iOS users must surely be chafing under the heavy heel of Apple's Evil Draconian Rule. The number of application classes that aren't allowed on the App Store is, in practice, pretty small--it's just that developers and other Hacker News fans are more likely to want/need apps that do run afoul of those restrictions. Even so, the amount of stuff I can do right now with apps installed from the Evil Draconian App Store™ would probably surprise you.