Here's my thought, if you happen to see independent smugglers doing business with pirates(as when they come to pirates' territory), you could just kick their ass hard, and independent wont blame you for attacking their fleet, cos doing business with pirates is not encouraged(or illegal as independent and pirates never get along) and should be "brought to justice". However when they moved away from the pirates' planet far enough and that is considered outside of the pirates' territory, you should not attack them as if you do so there is no evidence to prove they were doing business with the pirates, and independent would treated it as an hostile action.
