If you have the viewpoint for this location unlocked already, it makes things a lot more convenient! If not, when you dock with the Morrigan, you’ll want to work your way up to the stalking area across from the base of the ship with the viewpoint. From here you should be in the green search area and be able to spot the captain patrolling about with two bodyguards.
Kill the captain however you see fit and then head for the northeast corner of the zone. In this area you’ll find three marked enemies that you will need to kill. One often patrols away from the other two, so if you are in a stealthy mood, wait for him inside the nearby store house and kill him when he patrols in. Afterwards, quickly run out and double assassinate the other two outside.
Finally climb the building at the north of the area with the flag atop it and cut it down to end the settlement.