Well I would rather not have an auto win with the commanders death. Sure it signifies a significant blow to your team what with not being able to drop buildings/research, however you may still have a barracks or VF with which to push out and win with. If it was possible to make it map specific that the com's end could win a round that would be cool.
It wouldn't do anything for the first 60 seconds, and then it would drive into the enemy base. Empires turns into a game of who can kill the enemy robohobbes first