Is there any reason why civilian crafts cannot be sold after a successful combat mission besides balancing issues? It doesn't seem to make much sense to me that the gals would dismantle huge ships right down to its plasteel plates but simply leave perfectly functional civilian crafts lying around. Especially game-start, where you may be tight for cash.
At first, I thought that maybe the ship could be brought back to your base, somehow. Since the game, at least at the start, would detect that you do not have enough hangars (and your other ship is busy), it would prompt you to sell your newly acquired ship. Of course, that runs into the problem of you being able to gather a small fleet not soon afterwards (considering the obligatory nurse scoutings and base attack at the start).
If the ship cannot be brought back, then maybe it can be directly sold. Could the ship, somewhere in its tiles, contain the equivalent of its market price in cash chips? I recall the original game stored ellerium in the same tile as its functional engines, so you'd lose both if an explosive went off nearby. That makes sense, as theses little ships might be considered worthless if some piece of equipment inside of them stops working. The chips could be put in one of those tiles gals cannot get onto, like the control panel, and salvaged in post battle.
If neither turn out to not be possible, I guess the ship can be simply converted into scrap metal. The early scrap can be saved for a later project or immediately sold for a bit of cash. Either of these approaches would work, and might help you out in case you are needing to spread out the reward distribution in-game a bit more.