Could this be possible, perhaps as a box in the ships properties in FRED? It'd mean you'd be able to define colours on the Radar without altering the teams. So perhaps if you had a multi species Taskforce, you could mark the Vasudan Friendlies as a colour not already used by FS2 (Red Green Yellow (bombs) purple (Unknown) Grey). Available colours are things like Blue, Brown, Olive etc. or perhaps Darker/lighter shades of Green and Red to denote various factions within an an alliance, ie. Shivans could be your standard Red and HoL forces could be a Darker Red. Ideally, some sort of RGB input'd be nice, but I don't know if this'd be harder/possible.
It's not a big change, but it would serve to jazz up the radar slightly without needing to modify the way it works by much. As it is, it gives very little information - Using this method you'd be able to give at least a little more.