Judge Cote seems to think that the simple knowledge that Apple (and everyone else) had that the publishers wanted to raise prices was enough to show that they would know that the publishers planned to leverage Apple to force a pricing change on Amazon. For me, the problem with this argument is that it doesn't actually leave a way for Apple to successfully enter the market. Because any successful strategy by Apple would have provided leverage for the publishers.
The publisher were always free to raise their prices. The problem was, that if one publisher raised their prices and the other's didn't, that publisher would get screwed. By his own admission (goggle the DOJ slide deck for quotes and email) Eddy Cue went from publisher to publisher assuring them that everyone else was going to move simultaneously, as he had their commitment.
It was very difficult because each one wanted to be certain that all the others were really going to make the move before they would commit, a modern prisoner's dilemma. But Eddy got them one by one to promise that if the others would all do it, they would too.
In the slide deck there is a slide that shows how on a certain date, all the publisher's prices jumped up significantly. I don't know how else you can define facilitating a collusion that results in higher prices than that.
Had Apple just opened a book store and the publisher's took advantage of that opportunity, then I agree, Apple would be in the clear. But Eddy Cue masterminded the whole thing. That's where they broke the law.