At a controlled airport, ATC tells the pilot which runway to taxi to, and I just can't see a scenario where the controller would tell the pilot to taxi to runway 26 full length, much less a 26 intersection. I would be very interested to hear the ATC tape on this one...
Also, flow contol to ATL begins at 6:00am EDT 24/7/365 (at least for TOL...I have to assume LEX is the same way), so the tower would have needed to acquire a departure release time from Indianapolis Center's Traffic Management Unit for this flight, and I don't think they would be trying to beat the rush at all. Plus, I have to doubt LEX would have any other traffic (besides maybe one other plane or so) at 6 in the morning on a Sunday, where the controller would have to "shoot a gap".
The fact is it won't be hard at all for the investigators to determine the runway that was used. ATC tapes and the flight data recorder will tell the story. The runway theory will be confirmed or denied relatively shortly.
The local station is reporting, via Bob Orr of CBS news, that they do just that, and it's confirmed that the wrong runway was used. "Unnamed sources" warning.