GaoThe facility was pure chaos, as a general rule. Handling the Abnormalities felt like juggling way too many balls at once, and dropping one meant taking a train to the face, or any other disaster.
So while it was true that at first X had found Malkuth's demands toward her Agents way too harsh, he had to admit that having people who just obeyed was a life saver. If managing the employees had felt like herding cats he'd have snapped.