Hey, its the past calling, what if I told you that CR has operated under the Republic IFF for a very long time before this IFF-split happened (which we never wanted nor agreed to)? It also had a MIlitary IFF for all ships for nearly as long. And there were no issues because people apparently were able to apply common sense and treat ships according to their ingame tags and ingame behaviour.
Honestly, this whole 'you are Military and I rob or kill you' thing just looks like a giant pile of 'We are bored and have nothing to shoot, so lets come up with stupid excuses to get our fix of blue messages'.