Learning to recognize your targets in the battlescape is key in Piratez, from telling which gives bad scores to identifying which are worth risking your gals to get them alive and which is dangerous.
If you can catch the shipping before it lands, you can also look at the interception pictures. At least some government and rebel ships are distinguishable.
It is really tedious, but it is possible to stun all enemies (just make sure to revive one completely disarmed one, grab all their stuff (including elerium from destroying power sources) and then abort the mission. You haven't killed them, you haven't kidnapped them, so you don't get their negative score, but you have looted them so you get the value of the items + their stuff.