As you note, the circumstance surrounding this particular anti-trust case isn't the most clear, but I think it does make sense when drawn out a bit more:

Consumers were 'harmed' by the actions taken by Apple to approach and collude with publishers to break a monopoly that would benefit the publishers and Apple more than the consumers, even though the publishers felt they had no choice but to deal with Amazon and accept is loss-leader business model.

It doesn't seem rational that breaking up a monopoly would be worse for consumers, but based on the situation of this Apple/Publishers/Amazon case, that's essentially what was argued and the court system agreed at the end of the case(s).