Using recent mergers as an example, the two "pre-merger" forums are listed as sub-forums under the "new" airline but are closed to posting. The chief advantage to doing this is that old threads/topics are "closer" than if the forums are sent to the Discontinued Programs dustheap. You will find examples of this with the Delta/Northwest merger, the United/Continental merger, and the American/US Airways merger.
I think the difference here is the sense that this was not a merger of equals, but rather a case of Southwest taking over AirTran and thus AirTran ceasing to exist. I know that some people may take a different view of that, and I don't mean to start that argument, just pondering the thought process. If you go into Discontinued Programs, you largely find airlines that simply went out of business. AirTran seems to occupy a space somewhere between "ceased to exist" and "merged with an equal partner."