Anyone that has played TF2 or similar games is familiar with the 'Payload' game type. It is pretty simple. There is a bomb that moves whenever Team A has a person near it. Team A pushes the bomb to Team B's base. If they do, it blows up and team A wins. If the time runs out before Team A gets the bomb to the base, Team B wins. There are no other points, and kills are not counted.
Replace the bomb on tracks with an explosives-laden dirigible, and the players with ships, and you have a new game mode ideal for both Skirmish or Alliance. In Skirmish, it would be the first asymmetrical game mode. In Alliance, players could be on the attacker or defender side.
More options could be added to the GOIO version of the game, such as popping the bomb's balloon or destroying its engines to slow it down. It would be impossible to destroy completely, of course.
"I can just lay a zillion mines in front of it to lock the balloon down forever."
Not if the balloon is behind armor like a lot of the Alliance AI ships. This would also prevent Lumberjack supremacy. Actually, the Alliance AI ships would make perfect candidates for a 'bomb' ship.