Sure ultimately it was the publisher's decision to go to the agency model but if Apple and Amazon held firm it would have been a win for the consumer. Apple decided to take a swipe at one of its competitors which in the end hurt consumers by allowing for ebooks to be priced artificially.
eBook prices were artificial to begin with. Amazon was known to take a loss when necessary to set the price ceiling at $9.99, which (as you can imagine) would hurt competitors who couldn't absorb losses like that.