It appears that the management of Atlas has made a business decision to operate aircraft at a profit and not to cut a contract to the bone just to ensure an airplane flies. While that may seem odd at first blush; it is clear that should they have renegotiated at a lower rate, every other Atlas customer would have demanded the same. You simply cannot operate a business and charge less for a service than it costs to provide.
No doubt other operators will be jumping at the chance to fly cheap and hope to make it up with the profits or cash flow from other customers. Soon more will follow suit and eventually they will all end up cutting wages and benefits. Job losses will follow. We've seen this model repeat itself since the Deregulation Act of 1978, when the government refused to keep up the oversight required.
Atlas' most important move may well have been going outside the revolving door of airline management to find someone who is not steeped in the old airline operations theories.