There is currently no way to modify a custom faction or sovereign without deleting, or overwriting the file. And be sure to turn off cloud saves before you do delete one, or they will just reappear. I'm not even sure if a complete uninstall will clear the cloud files, suspect that it won't.
This is one of my biggest gripes with the current state of the game, as I'm all about building, and playing with and against custom factions. That this still hasn't been addressed is quite bothersome, especially in a game that is advertised as being customisable.
BTW, yea, Black may not be the best choice for faction color for the reasons you describe, but man, the units really look good.