Well, there is certainty a lot of back and forth on this.
To those that argue that the device equates to a mall and any app that provides additional content is a store front:
This analogy does not work to well. Customers do not buy a mall, they buy products in the mall. In addition, products bought in a mall are usable outside the mall.
Even if you say that the app store is the mall instead of the device being the mall, the mall does not control what price the stores in it charge their customers for products sold in the mall. My understanding is that apple will not let the "store" charge more for products bought through the mall. If this is a service that the customers want, they should not have an issue paying for it themselves instead of expecting the business to pay for it and pass the cost along to all of it's costumers. This happens in normal retail channels. Ever buy food at the mall from a restaurant / fast food establishment? They have to pay more for the space at the mall than they would somewhere else, but they do it because they expect the customers will pay more for the convenience of eating in the mall. This is the biggest point I see against what apple is doing.
To those on the other side of the fence that have stated that Apple is going to collect a fee for content purchased outside the app:
This is not my understanding based on what I have read. They are requiring that the content be available as an in app purchase, where they would get a cut. They are not saying you cannot get the content from outside the app however and they have no way to get a cut if the content is purchased outside the app.
A potential issue that was brought up by the blog that the original post links to is that currently there is a limit of 3000 or 3500 items for the in app purchasing system for any given app. This issue has been largely left untouched. The other arguments a moot if this is true since most on line book stores (certainly B&N and Amazon) have considerably more books than this on offer. I'm not saying it is true; however, if it is true and Apple makes this a requirement then it will be impossible for these book stores to comply. I do not believe there is any argument on this point, please feel free to correct me if I am wrong.
(Edit)
One thing I did not take into account previously is that for many books in particular they could not raise the price for books sold through in app purchase because of agency pricing regardless of weather or not Apple allows it; however, since Apple is aware of the situation (and for that matter was instrumental is it being setup) I still hold Apple fully accountable for the fact that there is no way for the online book stores to recoup the cost of doing business via in app purchase. If anything this makes it worse since they could not even raise prices across the board to recoup the cost (not that I would want to see that happen either but is is worse for the book stores).