It could be done in a number of ways:
Option A Use the ED as each teams score.
E.g. Team A eliminates all of Team B with 5 players remaining, so Team A gets 5 points, Team B gets -5 points
This would result in scores ranging from 7 to -7. With teams always having the negative value of their opponents score. The total number of points in the division should add up to 0, with the bottom half of the division having overall negative scores. Teams would get a bigger spread of scores as winning would not give you the max points. However there would be negative scores which might confuse the spectators, perhaps?
Option B Rather than using ED, use the number of eliminations the team made as its score.
E.g. Team A has 4 players left at the end of the game having eliminated all of team B, Team A get 7 points (number of B's they eliminated), team B get 3 (Number of A's they eliminated).
This would result in scores ranging from 0 to 7 for each team. So no overall negative scores to confuse the poor spectator. However the winning team would almost always get 7 points except in the case of the clock running out.
This could result in very similar scores for the top teams in large divisions. Although how many of there opposition they eliminated in the games they lost would still be taken in to account giving more distinction than the '1 for a draw, 2 for a transit, 3 for a win system'.
Option C Each teams score is the number of players they have in at the end of the game plus the number of opposition they eliminated.
E.g. Team A has 4 players left at the end of the game having eliminated all of team B, Team A get 11 points (4 points for there remaining players, plus 7 points for the B's they eliminated), team B get 3 (0 points for remaining players as they are all gone, plus 3 for the A's they eliminated.
This would result in scores ranging from 0 to 14, with the two teams scores always adding up to 14. There would be no negative scores and the teams would have a wide range of scores even for games they win, giving diverse total scores even in a large division.
For all of the above systems, penalty points could be applied easily.