whilst it is not made clear, my understanding is lore wise that due to the privalaged nature of members of the pilots federation, people are not encouraged to ever murder members of those, due to the the negative fallout of such acts (a bit like made men in the mafia I guess)
as such I do not think (and please correct me if I am wrong) that members of the pilots federation count for such missions.
I am not sure about that. And I don't recall the exact wording of the "kill trader" missions but, I don't think they mentioned anything faction-specific about the "targets" beyond the "trader" designation.
If I see missions like that I will copy them down for clarity so my posts here can reflect the specifics of those missions.
And just to be crystal clear, I have not, nor will I ever, accept those type of missions,,,,,,