The ones who are telling us to kill the Third Party soldiers are the Organization, who in turn take the soldiers who are slain in battle and hold them once they are revived. If they considered it more efficient for us to capture the Third Party, do you not think they would have told us to do so? We have no means to subdue the enemy and contain them for the entirety of a campaign; the Organization does not give us facilities on the battlefield, instead leaving us to set up our own. Dividing our forces to guard prisoners also reduces our efficiency to protect our own noncombatants and continue fighting.

I should also note that, while our primary objective is to kill the Third Party before us, we have also been subjected to secondary objectives such as saving survivors and keeping technology out of the the Third Party's hands. Tasking our forces with subduing and ensuring imprisonment of the enemy is difficult enough -- how much more when they are also tasked with the protection of others?