ebooks isn't the problem here.
the two most obvious responses from Amazon are, depending on the "keep the same price" question's resolution:
1. remove kindle for ios from development, or move it to jailbreak
2. offer two links in the ios kindle store, one for regular price, and one "through the app" version that's 40% more expensive (you know, to cover development costs to meet apple's new demands)
As others have pointed out, ebooks are sort of easy, and the real issue is other apps that use web links to purchase "app content" that in truth isn't "app content" at all, but generic content (things like skype credits, kindle books, ebay auctions, etc) being sold through an app. When you buy a kindle book, you own it on all of your devices. the "primary" intention is, of course, the Kindle.
Apple's stance makes sense for things like games (where you can "buy" a demo for 1 dollar, and then purchase more content through the app later...without their in-app rules, developers would be stupid not to take complete and total advantage of that loophole to incur a LOT more than 70% of the revenue.
But to impose this system on apps that are functioning as a store isn't going to work.
If Sony ebook store purchases fall under this restriction, then so do facebook credit purchases, or kindle store purchases. If apple enforces this on sony, or amazon, or google, but not facebook, then you'd better believe that the lawsuits will fly. Apple will lose.
In the mean time, think what would happen if someone like Mark Zuckerberg decided to call Apple's bluff on this policy and blocked ios from facebook until the policy was re-written...Apple would cave within a week.
It's one thing to have restrictive policies in a closed marketplace. It is an entirely different thing to arbitrarily and selectively enforce those policies on specific competitors. It has the same end effect as insider trading.