Not really, as I would argue that the e-books market pre Apple entering it, was inflated through unsustainable pricing. It's short-term thinking vs. long-term.
It's a complicated issue, no doubt, which is why we can spend so much time debating it. And, as is usually the case in legal cases, there is no clear 'right' or 'wrong'.
The publishers were unhappy with what Amazon was doing. Apple didn't want to enter the e-books market on Amazon's terms: what would be the point? It would have to sell e-books at a loss in many cases. It was a new service and to effectively compete it needed access to a broad catalog of e-books, thus it negotiated with the top book publishers. Did it know that it was very likely that the publishers would use Apple to re-negotiate their deals with Amazon? Sure. How could things really have played out differently? Cote and the DOJ see this as proof of a conspiracy to raise prices. I see it as common sense playing out, a correction to a model that wasn't sustainable but that was forced onto the industry by a monopolist player. There was no conspiracy needed, because it was pretty much the only way things could have played out.
But again, even it there were a conspiracy, the situation it created is more beneficial to the long-term interests of consumers I think than the unsustainable model that went before it. So why did the DOJ go after the small, new entrant and not after the monopolist? Probably because it felt price fixing was easier to legally prove and would sit better with the public ("we fight to keep prices low!" is a pretty easy sell). But that doesn't make it the right decision.