From what I remember the cleaners killed anyone they suspected of infection if they had it or not as seen in the mission on the first game at the makeshift town and others. As for the outcasts they where a direct spawn of Ridgeways actions after his units stole supplies from the people in the quarantine camps and gave them very poor treament to say the least. And to top it off shaw had all the jtf reports of ridgeways arrest destroyed that they found to hide the truth. Ridgeway as I see it was after power and controling caged people was feeding that need same with the rikers,lmb,black tusk going after civilians and other factions. For the most part the shd agents did not want to kill blindly as many recodings and eccos show so I will have to disagree with the op on this one as the shd is trying to protect what remaines(civilans and infrastructure) even with the bad actors in the shd and goverment.