If this does get made into a thing, and I'm talking waaaaaaaay down the track near the end of the final touchups and polish for the game, it could be something as easy as a pre-game sprite editor (a really basic editor with coloring being the only change). Sure, there's going to be people who won't use it because they won't need it; but the people who do want to edit their ships' color can do so to their heart's content. You could even edit the sprites right now if you wanted to by simply using Photoshop, but a Starsector ship color-er doesn't sound too bad for a final update.