Real reason, and this is from the Ybins - you need the Monokumas to get off the prison.
They were built and controlled by "Dr Iidabashi" - who also invented Keebo.
They got hijacked and reprogrammed by Shirogane, she kills them off as a preventative measure. You can see the Monokumas with Doctor Iidabashi if you know where to look, there's a full illustration of it