The best position you can get in to start this objective is to make your way up to the rooftop. This leads you work your way down through the factory and clear each floor.
Make your way to the highest point of the building. Go to the Southern edge and drop down to the next level in that area. This will lead you to a door that will get you inside the factory.
Just inside this door is a patrolling Blighter. Watch out for them so either take them out or stun them and then head to the North. Take the stairs down from there.
Once in the next level down, look to the South. You will find a group of 3 children you can rescue. Watching them though is a Blighter. Take him out at a distance or move in for a quick assassination. From there, head over to the children and interact with them. This will set them free.
You can also find the leader you are after on this floor. He patrols the Eastern side of the factory. This is between the far Northern end and the Southern end. If possible, eliminate him at a distance. This will cause most of the Blighters in the area to scatter and make the remaining portion of the mission that much easier.