Could there be some color customization? Just tweaking various colors on existing textures? Maybe paints? I agree with PetdCat that diversity goes a long way, even if it's small things.
Also, perhaps full custom texture palettes are out of the question, but what about single use ship decals or group (clan/organization) insignias or logos?
You could always set the maximum decal size to something small like 32x32 to prevent the majority of abuse cases, since graphic images won't show up well, and the few that do manage to fit something offensive in there will be fewer in number and could be reported by players.
I played an MMO that allowed uploading of a guild icon that would display next to every players name, I believe the maximum size was 10x10. But even something that tiny can still make the ship/group/team feel much more personal than selecting from a fixed pool of them in game.
Another possibility is requiring players to purchase the decals in-game. Say they upload the "design", but they have to pay an NPC to get it printed onto their ship, or whatever. That way people would be even less likely to try and get something offensive in there since they will be losing money when it gets deleted.