JetClipper... I think in general, you are right. However, I think as long as it has secured facilities and slots, etc, AirTran can operate MDW similar to BWI... which is to say somewhat out of the way of Southwest in a successful niche of their own...
AirTran will fly from MDW to BOS/LGA/DCA, Southwest will fly MHT/PVD/ISP/BWI.
AirTran will likely not enter MDW-MCI, and Southwest will likely not enter MDW-MSP (near term anyway).
I suspect there will be some overlap, like California and FLA, but I think they will offer two different products, like the difference between Southwest and America West at PHX.
Lastly, I think AirTran has the right aircraft and the right costs to do MDW well, where ATA had airplanes that were too big (175 seats on the smallest) and too expensive.
Oh, and lastly, while the initial deal has AirTran acquiring some assets, things are not necessarily complete. America West (speaking of them) have publicly said they may consider offering a second option to ATA's BK judge/creditors/shareholders. If you recall, RSA brought US Airways out of BK after trumping a deal between US Airways and TPG... So its not always the first deal that gets completed.
I have to agree, though, that whatever happens should be interesting to watch.