Don't know how something like this on the early main quest makes it through QA, but after hacking the scavenger leader to make him blind, and then doing a non-lethal takedown, this objective shows up even until I complete the quest.
I created an account just to post that I am having the same issue. I went for a non-lethal takedown and the quest does not update. I even tried shooting him in the head afterwards (in case for some reason, you actually had to kill him instead of using non-lethal to complete the quest), but I am still left with an incomplete quest.
also created an account to post that I'm seeing the same issue as OP. I also blinded and performed a non-lethal takedown.. then proceeded to shoot him in the face with that massive gun he had, threw him off the building into the street (where the trauma team shows up).. apparently he survived all of that though.
Maybe solved. Complete the objectives in chronological order. I skipped the Optional (take the path set out by) and went right for the scav leader. I was still able to walk through the door, but it never marked complete.
Reloaded and made sure to hit the path your partner prompts. Once it's checked, you can take the scav leader out in anyway you'd like, it will show completed.
When in doubt just do them in order, jumping around or bypassing objectives seems to create problems.
Sorry I had that bug too but still was able to move past this quest. Do i have to restart the playthrough now? I was able to get the follow up quests and just figured the quest does not close because the leader dies later on.