You're not supposed to linger there and loot, pay attention to the narrative when your character says let's get out of here. When you press tab to switch to grid map view you'll even see a blue dotted mission line heading down to the south portal. Fly there.

Once you're a little ways away from the scene, you'll get some more narrative so you know you're on the right track.

He is right that your not suposed to stay around but it should not creat permanant hostility (I encountered this cause I always stay to loot too. The trick is run away when your told too but go back as soon as one side wins. They will still say "plundering eh" and go hostile but if you run after looting and get to the next system the next mission prompt should make the hostility go away (they change your ID eventualy on your ship so you start with a clean slate with the MSF if I remember right. Looting in this situation should not permanantly effect your relations with either nesf or msf because of the later ID change. You will have to go through a hostile system or two to get to the ID change but thats purt of the mission structure.

As to StarFallMans answer. After THAT mission you don't get a new license plate for your ship.
The first time this happens is when you captured the pirate mothership! Thats a little bit more down in the storyline.