I think that may be hardcoded in, or burried deep in some insignificant file. It appears as though the setting for the pilots don't really apply to the players and a "hostile" player is always the top priority as soon as they show up.
If you want to play around with it, the file you need to work with is DATA\MISSIONS\pilots_population.ini (pilots_story.ini is for the SP main plot).
One thing I have been able to change is that I can make it so the AI ships won't be afraid to engage you, "I'm not engaging..." I suppose you could do the opposite and make them allways afraid to engage you, but then that's not much fun.
Take a common pirate job for example...
[JobBlock
nickname = tradelane_attack_job
wait_for_leader_target = False
flee_when_leader_flees_style = False
scene_toughness_threshold = hard <--- Change to hardest
flee_scene_threat_style = hard <--- Change to hardest
flee_when_hull_damaged_percent = 0.150000
flee_no_weapons_style = True
loot_flee_threshold = equal <--- Change to hardest
attack_subtarget_order = anything
field_targeting = high_density
loot_preference = lt_commodities
combat_drift_distance = 25000
attack_preference = fighter, 5000, guns / guided / unguided
attack_preference = freighter, 5000, guns / guided / unguided
attack_preference = transport, 5000, guns / guided / unguided
attack_preference = tradelane, 5000, guns / guided / unguided
attack_preference = weapons_platform, 5000, guns / guided / unguided
attack_preference = destroyable_depot, 5000, guns / guided / unguided
attack_preference = anything, 5000, guns / guided / unguided
Changing the lines I marked to "hardest" will keep them from running and make sure that if they disrupt your tradelane they attack you. If you're curious, I did try messing around with the attack_preference settings but there must be an invisible line above them all that reads: attack_preference = player