I think the primary problem with the ebooks lawsuit is that the DOJ and Judge Cote was thinking of them like they were physical books. Apple and the publishers were also prosecuted for quite narrow price fixing (new best selling books) to boot as the average selling price across all books declined. I'd be more apt to back the DOJ if it was over physical books sold in retail shops.
Obviously they are not physical books. They are a digital good, not only that, they are currently a digital good with DRM that seems very dependent on a certain kind of hardware (tablet) to be successful.
The ebook market today doesn't really exist without the players that can display the ebook. ebooks basically failed to become viable until tablets (Kindles) became a reality. So, the addressable market appears to be sized to the number of tablets in the market, not to the number of desktop or laptop computers out there. With Apple's iPad, it increased the addressable market for ebooks, what, 10 times? How many Kindles were sold in 2009? 1m, 5m?
Apple sold 15m iPads in 2010, 40m in 2011 and 66m 2012. Not only that, Apple made the prototypical tablet for all other OEMs to design from, and those tablets sold in as significant numbers and for much cheaper than the iPad. Amazon responded to Apple's design by taking Blackberry's Playbook and rebadging it as a Kindle Fire 18 months after iPad 1 went for sale. The Kindle Fire [HD/HDX], an iPad form factor device not a Kindle eInk device, is the flagship Kindle today. Is that not the very definition of pro-competitive?
With lots of tablets in the market, there was a large market to sell digital goods to, a large market for ebooks. This means more competition. New retailers can arise. Publishers can become retailers. The retailer can be the publisher. Self-publishing becomes viable. Mass market ebook and niche ebook retailers can co-exist. That's a gigantic boon. A huge economic benefit for consumers and sellers a like. The very definition of pro-competitive. If Judge Cote and the DOJ wanted the ebook market to return to what it was like in late 2009, well, wasn't the proper solution for that to have Apple remove ebook functionality from the iPad. It was after all basically an afterthought for the device they developed in about 3 months just prior to launch. How about ebooks should only be sold on eInk tablets like the Kindle or the Nook or the Kobo readers? That was the state of the ebook market in 2009.
Secondly, yes, Apple enabled publishers to raise popular books (generally of the novel and hardcover style book, not text books, not books with color, etc), but these ebooks were still subject to price-demand curves. An ebook has "infinite" supply. Demand was low and will be continue to be low for ebooks relative to apps, music, videos, web browsing and games. People don't have to buy an ebook at the publisher's price, and they have a lot of other options, especially in the LCD tablet market. The price was going to go down.