They should always let you haul the scorched wreck back to port, and pay a tremendous amount in terms of credits or supplies to repair it. There should be an up-front high cost in terms of supplies just to stick the parts back together, set up tractor beams, etc, and it should be high enough that there's a good probability you won't be able to afford it. Some of its equipment will likely be destroyed beyond repair.
As they say, where there's a will there's a way. I can imagine a lot of admirals being too damn stubborn to get rid of a ship, no matter how broken and torn up it is.
I think having a high cost in supplies would make this balanced and themely, although one wrinkle I see right now is that your casualty report is currently handled before looting is. Meaning, if you hit a trade fleet that's packed with supplies, you won't have those supplies to repair disabled ships with. That might make perfect sense however, if you consider that this is kind of an emergency triage-type thing.
Perhaps eventually, once skills and officers are added, we can have a pool of 'first aid' points that allow us to bring back disabled ships with certainty. When you take a beating, you'll have to decide which ships you'll save and what ships you'll consign to the boneyard.
All in all, I think this game requires you to save before every fight too much. Once there's some sort of experience-gain mechanic in, then at least we'll have something to show for it, but right now if you lose a battle it's just a total pointless loss.
