It was a week of disappointment for American and JetBlue, who spent the time digesting the ramifications of a judicial order to end their northeast alliance. By all accounts, it was working well for both carriers. American did downplay the impact in a presentation to investors last week (at a conference hosted by Wolfe Research). It said the ruling will not materially impact earnings, though it does throw a wrench into its New York strategy. JetBlue will feel it more. And besides, another big legal fight remains: Will the Justice Department also get its way and put a stop to…