However realistic such an option may be, I think it takes away from the freedom of the player, which is why I don't like such a feature (also hated it in the Total War series, which is why I didn't play those games much).
Of all the problems with Total War games, I actually think morale was one of the things they got right most of the time. Only problem I had with it was that in certain games, on the highest difficulty levels they give the AI ridiculous morale bonuses, which basically meant you needed elephants and flaming ammo artillery to get good units to retreat.
That said, yeah I'm not sure how it would work with Sins. With total war it works alright because your troops are always grouped together information. In Sins the individual ships are more independent, making it harder to decide which ships should be retreating. Also, in Sins the entire galaxy is a battlefield, in total war its just a few random square miles of land.