I know what you mean, AC. Not mentioning any names, but its slightly dumb for half of an attacking force on Crete saying they bombed this and that not to be getting shot by our NPCs. Makes it a bit unfair, as you said.
All of my TBH characters, while they might not be hostile with the BAF, Outcasts or whatever, will shoot them to get them hostile before an engagement if possible. For example, I start shooting BAF in my GB around cambridge if they happen to be neutral (even if I am not about to engage, but I consider this a courtesy).
It does pain me to see people not being attacked by the NPCs they should be. That battelship should have killed the Corsair so fast with its battlerazor-like guns, being on the recieveing end of them is not funny.
I wish Drake's suggestion could be implemented, it would solve alot of problems. It may create new ones in the process, but I believe this is more than a fair trade-off.