Might have mistaken your situation with someone else who avoids civilians like the plague, they have the same negative score for capture as killing, but are pretty good subjects for research and/or ransoming.
When you intercept a ship and it says "Civilian Traffic" it usually has people that dont present a penalty. Bootypedia says they're fair game.
Usually its something like a Saavy Girl, Tough Girl, Tough Guy, or Sharp Guy. You get a tiny green aircar that has 2 people in it, or you get a midsize green aircar that has 4-6 people in it. Or you get a cool looking green 2 floor spaceship that has a tough guy and a saavy girl.
I mean you dont get much points on the debriefing screen for them (maybe ~40-60 total) but you definitely dont get a penalty unless you kill them. Penalties for killing dudes is usually like -4 to -7 per dude.
Also apparently just shooting down the ship provides at least 100 points each because at the end of the year I can still be like 1300-2300 points scary even though I distinctly do NOT remember getting anywhere near that from my mission debriefings (40-60 points here and there, it adds up but not nearly that much)
These usually go about 1000mph or so and they have no weapons. Sale proceeds from loot and ransom is ~50,000 to 200,000 depending on what you want to keep.
I have run into a few missions where you have something like a small transport ship with people in brown uniforms,
you get a penalty for the people on board - whether you kill or capture them it doesnt matter.
But they arent marked "civilian traffic" and the interception image doesnt have the (orange and blue?) lights on the front that the bootypedia says is a Rebel Freighter (which also says you're not supposed to shoot it down).
I havent encountered those much though, only the rare ones that land (intercepted one and didnt want to get shot, and then it landed nearby, so I remember what the interception picture looked like). Only enough to know this is a thing.
