As the saying goes, "If you're not sure you can annihilate the Green Skins, don't force them into a corner." If you split up your Fleet to pursue them regardless of how the Green Skins divide their squads, there's a chance they'll turn around and knock you out if they see their pursuers aren't as formidable.
Securing the current victory is already quite an achievement.
Plus, though half of the Green Skin ships escaped, the loss of combat power is far greater than that proportion.
In the pursuit, since it's already clear that it's impossible to eliminate all the Green Skin ships, the focus naturally shifts to targeting the most valuable ones.
The Green Skins' two heavy cruisers were done for in the previous Fleet showdown. Of the remaining five ships comparable to Human light cruisers, only one managed to escape. The rest were all destroyed!