My thoughts on this issue:
At the core of the issue is the Most Favored clause.
Apple wanted to sell book but wanted the price to be always the same price as other online e-sellers. Apple however does not want to be in the book selling business and figure out the pricing. The solution to that concern is simple. The publishers set the price of the book on the store and Apple gets a 30% cut. Apple does not care what the publisher sets for the price.
The kicker is that at $9.99 a book that was less than what the publisher think is a good price for the book based on their view of what it should cost to recover the costs of publishing the book. The publishing process has lots of fees, so while you might think write and sell is all that happens there is a lot more. The $9.99 price brings the average price they need to maintain to make good money.
When Amazon was the king of books, the publisher could raise the price of a book to get more from Amazon, however Amazon would take less profit, no profit or even a loss of the book to maintain the $9.99 price. The publisher was actually happy with the price and Amazon sold more e-book readers.
When the Apple contracts kicked into gear, the publishers wanted to list the books on iBooks, but the publishers wholesale price of the book was higher than the Amazon price. However with the "Most favored" clause in the contracts they were obligated to let Apple sell the book at $9.99 and take the 30% commission of $9.99 with a payment of the remaining being 70%.
Here is the kicker, with the Apple pricing model and store model it was the publishers who were taking the loss not Apple. The Amazon model, always paid the publisher the price they set even if it was more than what Amazon eventually priced the book. The Apple model had the publisher set the price and Apple get's 30%.
The publishers did not want to take a loss, they liked the Amazon model. It was working, but how can you ignore iBooks? They took Steve Job's advise and forced Amazon to price books at their prices to allow them to put then on iBooks and not take the hit on their margins and not be forced to see books through iBooks at a loss.
The Amazon model works well for Print books and have to manage the physical books more like traditional inventory. The management of traditional inventory has risks and other costs that don't relate to e-books. The e-Book is not as cheap to produce as you might think, especially with DRM. Another method of dealing with e-books needed to be vetted. The Apple model turns the publisher into the seller with the e-book seller as as passthrough and marketing front.
The Apple model is actually better for the e-retailer, in that they have less risk, which is why Apple likes this model.
In the end the Amazon model was not likely going to last forever, the publishers don't want someone selling the books for less that what they price on the wholesale market. The Apple model is good for the e-seller because it creates less risk because there is no real inventory.
The real loser is all of this is the consumer. The e-book is over priced, not because it costs less but because it has no potential resale. It is hard to pass the e-book on to friends. If someone likes a book they might tell a friend but there is no way to pass a book to a friend after you have read the book. (Well no legal way). Amazon knows this which is why they sold the books so cheap.. they where going to sell more copies of the same e-book and likely another Kindle in the process.
Apple is not using iBooks to drive the sale of the iOS device. They just want to have a books store to have a complete package. However they don't want to have the highest prices. Which is why all this started.
The real villain here is the publisher. They need to understand better how to deal with e-book and understand they if they price then right then they will sell more and make more money. The problem is that book publishing is old and traditional and the e-book is new and confusing to all the guys in the leather chairs at the tops of those high buildings.
I think they probably did fix prices, but not because of Apple telling them to fix the prices, but because Apple told them you can't afford to not be in our store and if you want to be in our store, you have to take the risk on pricing not us. They publishers did not want to take less than what they were getting from Amazon. They had to force Amazon to raise prices so that when they sold the books on iBooks they made the same profit.
Publishers wanted to force Amazon to raise e-book prices. However Amazon was the only real e-book seller in the USA. So when iBooks was released the publishers finally had the leverage they need. They would stop letting Amazon sell their books and sell then (at their risk) at a higher price on iBooks. They won because they get a place to sell e-books (now with Apple) and Amazon who depends heavily on e-books had no choice to agree or loose the catalog they needed for the Kindle.