If the craft contains valuable loot and you have good means to control enemies, you can go in, grab stuff (gold?) and get out. As long as you don't kill/stun all enemies, the mission will continue.
So if you stun all but one (kept awake, preferably without weapons from being stunned, disarmed and revived), you can manually haul all the loot in the Bonny (armors, gold, weapons, even destroy the engines to grab the fuel), then "abort mission" will not count the stunned enemies since you did not recover them. You will only get the positive score for grabbing items.
This is more manageable once you have decent weapons and gals, and on small crafts, but provided they aren't armed with heavy or advanced weapons, it should be doable. And it's an interesting change of pace, trying to subdue but not kill people and taking off with the loot.