My thought was that a team must hold a minimum number of the top spots for the victory condition to trigger. 51% is probably better, as it would work for even numbered groups. So if a team was made up of three players, then the leaderboard must have two of them as ranked 1 and 2. The third could be lower. If there are four players, they would need to hold ranks 1, 2 and 3 before the victory condition triggers.
I agree that eliminated players should not be held against the team. If a player needs to leave the game, or is eliminated while the others are able to survive and make a comeback, they should get at least partial rank points at the end. Maybe how they exit should determine the amount. Being eliminated should be viewed as better than conceding, which should be better than AFK.
I think each player should have their own empire, but would like to see shared carriers, or at least have them retain their waypoints as they cross lines. I would be willing to pay extra for special carriers that could be jointly controlled while keeping standard carriers for collection purposes.