Ben has stated "we're the good guys". Maybe he's right? Perhaps the purge was to get rid of everyone (harsh as it sounds)that the Nemesis might take over. Ben saw his dead mother in the jungle and we all can guess now that it was Jacob (or Nemesis) using the form of Emily. The purge was brutal from the viewer's point of view BUT there has to be a darn good reason for it. Maybe Dharma had the sickness Danielle spoke of. And Richard, as peaceable as he seems - he was right there gas mask and all. So I think the purge was a nemesis preventive tool.