Thinking about it, in VB6 I believe FDF fire would activate for missiles targeted at yours and allied ships, but not for those targeted at neutrals. If this is correct, and still the case in C#, then canonically a missile's target can be identified at FDF range. In this situation I don't think the diplomatic status of the race who fired the missile should be taken into account...
Maybe there could be a special exception for captains who are low scoring in everything except the Political Reliability bonus 
"No! Hold fire! I must think of my career! KABOOOM!"
Yes... for final-defensive fire I certainly agree that those should fire if any missiles are impacting one of your or an allies ship. But AMM should only fire if the incoming missiles are marked as hostile first.
