Late to this debate, but I like the OP's idea. but make the map
concentric circles instead of squares, because squares have corners, which are problematic exploits. Freighters in the snoozing zone would automatically wake up and start depleting CR/supplies if enemy ordnance or ships approached them. This is why you should leave some escorts sleeping with them.
cf a post I made a while ago that is vaguely similar to this:
http://fractalsoftworks.com/forum/index.php?topic=10591.msg181633#msg181633Since warships already have overpowered civilian capacities (passengers, cargo, fuel storage) these would be nerfed to make civilian ships useful. The nature of the game would change to something I would like more, and which some people would like less.
Putting all this tactical complexity in the pre battle dialogs defeats the purpose, since then you're playing a simplified text adventure instead of a real time strategy game. And those dialogues are boring and confusing.
Retreating into the 'nowhere' zone is still a bit cheap even in your system. Honestly if things were to be redesigned from day 1, the campaign map should keep ticking at like 1/60th speed during combat, and retreating ships should become a separate fleet bubble on the campaign map that'd be vulnerable if your fight dragged on too long, and which you'd reunite with after the fight. In this system people could also leave their civilians as a separate fleet hidden in a nebula nearby, but then they couldn't use them to store plunder etc.
However the game hasn't been designed to sustain performance for all these ideas, and it's too late big changes, or SS will end up like one of those never-finished Orson Welles projects. This is the major conceptual problem of SS' piecemeal progression: Combat 1st without a clear conception of campaign, and now we have two separate games which are both fun, but the way they interact (stapled together with those painful dialog adventures and the IRS lovechild CR system) isn't all that smooth or fun. However perhaps more things to do in campaign will make this less noticeable in the future.
If not, there's always StarSector 2.