Ah, well, if that's your problem, there is a thing that can help with that if you want. Look at it like this:
You see, all us players, we are all part of the "Elite", members of the Elite Federation of Pilots. Yes, even the n00bz. NPCs are not as awesome as we members are. The EFoP don't lay down too many rules, its mainly a rating agency and social club combined, although we are all meant to be superb pilots, much better than the hoi polloi.
Our scanners are capable of identifying other members of the EFoP for us. Letting us know we might be attacking one of our own - although the EFoP, while frowning upon this sort of activity, does not actively punish it. After all, its a dog eat dog galaxy out there.
How's that? Immersion restored?