People aren't even talking about the actual situation, which has nothing to do with in-app purchasing.
What Apple did was to
require Amazon to REMOVE a Safari link to their OWN STORE from within THEIR OWN APP. (Before and after pics below)
View attachment 430409
After that forced removal... which came AFTER THE APPS HAD ORIGINALLY BEEN APPROVED... a user who wanted to buy a book from the Amazon Kindle Store (or B&N Nook store), had to exit the reader app, open Safari on their own, buy the book, then reopen the reader app.
In stark contrast, Apple's own iBook app is allowed to have its Apple store integrated, to make it more attractive to users.
Even a child can see that this was clearly an Apple attempt to unfairly gimp their competition.
Therefore, the DOJ wants Apple to allow Amazon (and B&N, etc) to put their original Safari links BACK in, so their customers GET ALMOST THE SAME CONVENIENCE AS IBOOK customers have.