What you suggested is already available in some kind of mod. Not sure, which one...
What can be really better - capturing enemy officers. You can release them in they faction market for some rep, or sell them on market of factions that are hostile to prisoners faction for reward and additional rep penalty with prisoners faction. Also you can try to converse them in your religious hire them or simply space them out in airlock for fun!
New mission type could be added - bring target officer to justice alive. Twice as distance traveled, twice as paid!