That is some solution, but not without flaws.
As it is right now, when you see a white rectangle with a name - you know it's an enemy. You don't have to focus on it, mere glance is enough to know.
Your idea breaks that a little, unless, I don't know - allied spot has completely different color; which still doesn't change a different fact - it might litter the bloody screen.
Also, this still screws with the idea of general communication between captains and crews mentioned earlier.
This is how I see this, I mean - first things that comes to my mind from a gameplay design standpoint. ^^