A tiny suggestion: add an infrequent check that SM-repairs-all civilian ships.
During a recent incursion into the Sol system that caught me with my main fleet elsewhere, I scrambled whatever I had on hand to defend - including a recently completed batch of ten railgun fighters intended for my new carrier, still on the ways. While they couldn't bring the fight to the enemy, they COULD inhibit their missile attacks, and did so - I used them to escort an unlucky civilian cargo ship and they handily shot down every salvo. Only one leaker got through, punching a hole in the freighter's armor and taking out the cargo bay.
As an experiment I let this ship alone, and sure enough, a few times later, I noticed an error message indicating that the freighter in question had failed to pick up a civilian contract load. So I tracked it down in the civilian ships list and SM repaired its cargo bay.
Civilian ships being damaged but not destroyed is of course rare, the remedy is at hand and it even throws an event message. So this isn't exactly high-priority. By the same token, there seems no good reason
not to let damaged civilian ships (at sensibly infrequent intervals) automate pressing the "SM Repair All" button. If this could cause problems elsewhere, it's certainly not worth it, but if the occasional civvie ship with a nonfunctional cargo bay could throw an error in other parts of the civilian contract code, it might be an edge case worth plugging. I wouldn't know, I haven't seen the code.