Hey, I had the same problem and decided to really dig my heels in to figure out why it was not detecting them as alive. I also choked them all out and did not hide any of their bodies. There was one deciding factor that seems to have allowed it to succeed. There is one choom just outside of the building, if you leave him outside the "mission area" the moment you enter the mission area, he dies. So take him out last, make sure to drag him inside the container until it says "hostile area" BAM mission completed without deaths.
Hope this helps!
That is apparently what happened to me, thank you!