Getting the later flight out first allows a few things:
- Delta keeps its on-time performance indicator higher;
- Less misconnecting passengers. The first flight is already screwed and everyone has misconnected. The second flight might be on-time or only slightly late and most people can make their connections;
- The equipment from the first flight is now not going to make the next flight it's scheduled for so that ATL-xxx flight is either delayed, cancelled or an equipment swap happens. The equipment for the second flight has a better chance of continuing to the next destination with little or not interruption (assuming the weather improves in ATL, of course).

There are many valid reasons to let the less-delayed flight leave first. Sure, it stinks to be scheduled on the earlier one and watch a flight that was scheduled to leave after you actually leave before you but from an operational perspective it makes perfect sense.

-RM