We investigated an approach to this very early in development that involved drawing a hull paint layer which could be coloured by code. I imagine the player would get a slider to change the hue, basically.
It was ... it was okay. To make it really work I'd have to take some personality out of the hulls, and doing an additional sprite layer for every single ship would be a bit of a pain. We handle friend vs foe identification through symbolic overlays now, as y'all of course know.
I did find the test shot I sent Alex - check this out (from July of 2010!).