If the merger falls through, AA already has a contract with its pilots that is largely AA management's proposal for operating as a stand alone company. The judge voided the contract and allowed AA to impose its terms. That didn't change that the union represented the pilots; it just meant AA's terms applied until AA and the union negotiated a new contract. They then quickly entered into a new contract.
AA didn't ask to get rid of seniority or establish a meritocracy for pilots. Seniority works well for managing pilots. AA's structure for using seniority is pretty similar to that of B6. AA's concern was the work rules ... what rest seats pilots get, scheduling, how many pilots they use on long haul flights over and above FAA requirements. They largely have what they wanted so if it doesn't work, AA has no one to blame.
The unions negotiated side deals with US that are better than their deals with AA. So, the unions want the deal to go through. They are unhappy and applying lots of pressure to the White House and there seems to be some suggestions that the DOJ will throw the case or settle easily. In fact, some of the DOJ's statements seem pretty half-hearted.
If the deal doesn't go through, AA's contract with the pilots will no longer keep AA from being competitive or expanding.
And ... disappointingly, none of the consumer issues the DOJ has raised address the impact upon frequent flyer programs from diminished competition.