I don't think so. One thing you could do is change 'destroying enemy seedlings' to 'participating in battles'. When a seedling is killed, the points that would be gained from that kill are divided between the other factions on that asteroid.
For example, if there are three armies in orbit aroid an asteroid
A, with 100 seedlings on the asteroid
B, with 200 seedlings on the asteroid
C, with 50 seedlings on the asteroid
A kill is worth 1 point
If a seedling from A is killed, then Empire B gets 1*(200/(200+50)) = 0.8 points. Empire C gets 1*(50/(200+50)) = 0.2 points.
More generally, the points awarded to faction F when a seedling from faction X are given by
PointsPerKill*(FSeedlingsAtAsteroid / (TotalSeedlingsAtAsteroidThatAreNotFromX))