We also booked Airtran airfare through Disney's CRO, and only received the Disney confirmation number.
The Disney agent specified that they would be paper tickets (not e-tickets) but she wasn't sure when we would receive them. (She was also somewhat surprised they were using paper tickets).
Our trip is in September, so if it gets within 3 or 4 weeks and I still haven't gotten the tickets I plan to investigate at that time.
From the Airtran website I found:
*Please note: If you originally booked your reservation through Expedia, Priceline.com or LowestFare.com, please call us at 1-800-AIR-TRAN for assistance with your reservation.
Maybe the above applies to Disney booked reservations also.