Hidden-city ticketing is not prohibited on AirTran. Of course, it's not a practice the company promotes, but if you find a lower fare to a connecting city even if Atlanta is your final destination, you are welcome to book such a ticket. Unlike on legacy carriers, the rest of your itinerary won't cancel out if you don't fly all segments, so you can even book the hidden-city ticket as a roundtrip if desired. If checking bags, just tell the agent that ATL is your final destination and the bags can be tagged as such.
FL and other LCCs are generally very flexible in this regard.