Instead of morale, what about pilots being cloned/un-cryo'ed at a certain rate. "Available pilots" would be a sort of resource whose income could be increase by science and/or assets.
I don't like the idea of having human lives at stake (even if "it's just a game"). But if it's going to be a thing in AIW2, I wish it would be much clearer and mechanically coherent. For instance, in AIW1, there is a sense of "death of Humans induce AIP": cryopods, bubble cities, rebelling colonies, etc. But not for colony ships and orbital command stations (but there is the shark plot). While I would prefer to not have human lives at all in the game, if you make it, make it completely.
On a more technical note, I like reprisal/salvage as it is and I don't see the need for improvements here. Wether that "morale" (or human lives) mechanism is an improvement, that's another question, and for now I vaguely think it's not.