Um no one is giving up any liberty. Apple is sheltering the uneducated until they are more learned. That is all.
If in five years I can only run apps on my Mac that come from the App Store then I'll eat crow but I'd bet everything I have on that not happening which is why I am a iOS and Mac developer.
I understand. Without talking to the author directly we'll never know if he especially crafted it to be received that way.
Personally I feel this is just the authors genuine opinion/enthusiasm for this topic coming out on paper. I think he believes (just like I do) that this should be the "norm" and is a correct step forward. I see this as how I would have a conversation with my parents and explain to them why Mountain Lion is going to be so great for them. Obviously I would be crafting the conversation to lead them towards this being the "norm" because I think it should.
But again I am bias because I basically agree with the author whole-hardily.
If in five years I can only run apps on my Mac that come from the App Store then I'll eat crow but I'd bet everything I have on that not happening which is why I am a iOS and Mac developer.