Sorry if this has been mentioned a zillion times already, but I only just noticed this myself.
I went with the take Marie > go to Wernher > Take Marie back to Ashur route. I didn't kill the raiders at the entrance, instead I shot the Infiltrators from their hands so I could take them.
Just went back today and the 3 raiders at the entrance are the only raiders in the Pitt that are hostile to me. Plus, they once again carry Infiltrators. I thought I could only get 4 of these,
but now I wonder if they keep respawning.