ORIGINAL: Chris H
Simple, return fire only. Set the RoE as TIGHT to neutral target, and your unit will only return fire at neutral targets when they attack first.
Even in real life event occurs such of intrusion like this, most of the time are not going to attack incoming neutral units unless either having extremely bad relationship, or mistaken as hostile by faulty Intel gathering (easily happens at no-fly zones when war happens).
That will cause attacks on all targets. If you have something coming towards and you suspect it's an attack run use the H key to mark as hostile. If they turn out to actually be neutral they will revert back, hopefully before they are fire on. Look at using the H key as a radio message telling them to veer away.
Oh, doesn't knew that feature though. While I am playing, the unit will have number indicator to tell me how many missiles are coming toward it. That is the most certain point the target is attacking my unit.
Think again however, I am highly doubt that player's unit will just be casual and ignore them when neutral units nearby had fired a shot, either random misfire, or attacking 3rd side units. A knee-jerking reaction to 'return fire' is still legal to the RoE, even it will lead into uncontrollable outcome.