I had talked to Keyvias about this earlier, as I happen to know a lot of color blind players.
Having an option to toggle the colors of the actual in-game models is an excellent idea, but the game wasn't built with that in mind, so it would be quite a beast for the art/programming team to go back and retroactively implement. Also, the general (mostly unofficial) consensus was that the in-game ship colors would likely not be changed, as they are supposed to be somewhat ambiguous, especially at longer ranges, and spotting helps to counter this.
However the HUD and map colors could/should have a color-blind mode. The HUD and map should be clear and readable to all players. The map arrows, and CP indicators are intended to be immediately distinguishable, and that is not always the case. Additionally, the people I play with have trouble on maps with a green background (Paritian/Labyrinth), as the red/blue map arrows and HUD elements blend in far too easily. This would also likely be much easier to code into the game. Furthermore, if there was an incident where the game models were hard to distinguish and spotting was not possible, simply pulling up the map and noting if it's a friendly ship should help with any confusion.
There was a question that was raised, without an obvious answer. What colors would be good for the HUD/map? Making the red more 'orangey' was the best suggestion we could come up with, as was making your teams HUD/map elements slightly "pulsate" (like your own arrow does on the map).
So lets get some discussion going here. Does this issue affect you? Do you have any color combination suggestions?