Perhaps if Amazon could sell iOS apps, they would only take 20% from the devs. But there is only one iOS app store, owned by Apple.
Of course Amazon can only sell iOS apps Apple approves of, just like game consoles. Amazon can only sell xbox games MS approves of. So saying a second app store would bring malware is not true.
Apple is currently acting like a broker. The app developers do not charge Apple a set fee for each copy of the app and then Apple sets the sale price. So, if it moved to a more retail-esque situation, then a developer would pay Amazon to be part of the store, and Amazon would sell their app at whatever price they want (why would Amazon, or anybody, allow you access to their customer base for free?). Looking at book sales - publishers/authors aren't losing money on each sale below the MSRP. But that set up is much more complex.
I completely understand your point, I just do not think a court could compel a company to do it. I also don't think that lower prices app prices are good for developers (I say clean out all the junk and charge more for good, useful apps). Currently the App Store restrictions don't go against my sensibilities, so I am discounting the importance of them - which may be a much bigger sticking point for others.
This isn't about free apps.
Imagine adobe made a full feature photoshop app for iOS and they want to get $70 per copy. Since Apple has a monopoly on iOS app stores, the final price will be $100.
What if Apple didn't have a monopoly on iOS app stores and Amazon could sell iOS apps. Perhaps Amazon would only take 5%. The user can buy from Amazon for cheaper and the dev gets the same amount per sale. Wow, competition at work.
Businesses generally bake all of their costs into the sale price along with profit margin. In some instances you can lose money if development or recurring costs are higher than budgeted, but Adobe would never create a _new_ product for iOS without baking in the 30% fee already. So, if they wanted to make a $70 iOS app, then they'd make sure it only cost them $40/copy to design & market + $21 app store tax = $8 profit per copy sold. This is different from the Mac App store (where prices likely would increase) since pricing was set prior to the 30% fee being taken into account - this, in my opinion, is why the MAS has so many apps sold outside. Also sandboxing and all that really changed the game for Mac app developers, who may have had to rethink their entire app based on the new technical limitations.
And if the Apps still had to be approved by Apple, there is nothing saying they still wouldn't charge $99/year + some additional app review amount (its like a couple grand to develop an XBOX game I believe) so this would really impact bootstrapped developers who need to pony up money before making a single sale.
Case in point - please see Amazon not paying the developer at all when was doing the "free app of the day" or whatever, back in 2011. They have since discontinued that program for Amazon Underground.
https://gigaom.com/2011/08/02/54805-reasons-not-to-be-amazons-free-app-of-the-day/
Ultimately this decision only says the case could be taken to trial, and maybe it would be good for the development community & consumers in general...my personal belief is that it will not, but I can see the other side of the argument too.