Whatever had been done to them--or perhaps the absence of a true soul, whatever that was--left them rigidly bound to their past ideas and totally incapable of doing more than following orders by routine now.
What they did to them was terrible and sad. 
mnli hypothesis: What they did to them was terrible and sad.  premise: Whatever had been done to them--or perhaps the absence of a true soul, whatever that was--left them rigidly bound to their past ideas and totally incapable of doing more than following orders by routine now.