I'll just go ahead and say,
When there are duplicate ships on both teams, its pretty hard to tell.
Back before patch 1.4.0, all-pyra battles were all too common. With all of them being close-range metamidions, when you approached an ally-in-engagemet, the only way to quickly tell was by whether they were shooting at me or not.
Also, I fly a maroon Mobula named Porco Rosso. Due to its reddish color, I've had complaints when I was on the blue team.
So, I get where the guy is coming from. However, I like it as a feature. Too many multiplayer-first-persons are too simple. Red or Blue shirts, Red or Blue Team markers, Red or Blue power armors, are unrealistically obvious. Having to communicate with your team mate "Ally, don't shoot." is part of the game.
Having said that, if I see one more friendly mine, I will $&#* @^*% &).
And if I see a friendly mine in future co-op games, I will %!*# H*@ ^#!# &) ^*@ #((!#!.