Okay, here's my theory. Rozer is actually the one pulling the strings on the ship, while a cohort on Kerbin pulls whatever strings they can pull at KSC, with the end goal of either completing the mission with maximum efficiency, or ending the mission early. In the new software update, they may have included a system that Rozer can activate which will cause BERTY to malfunction, resulting in mission failure and having the failure be blamed on BERTY. Rozer and accomplice get off scot free. Or, they could have simply removed various ethics systems and morality code to increase the efficiency with which BERTY operates. Losses are blamed on the AI taking excessive risks, Rozer and accomplice still get off scott free.