I think that is a little unfair on the controller at Lexington. The two thresholds were effectively in the same place viewed from the tower. The flight crew chose an unlit GA runway rather than the lit main runway. Visibility over airports at night is confusing at the best of times. By the time the controller could have recognized that the aircraft was attempting takeoff on the short runway he could have said nothing to prevent the accident.
FWIW, I re-read the NTSB final report once again and I think it's fair to say the board believes that having only one controller that morning -- against FAA guidance -- was an additional factor in the accident:
The controller further stated that it might have been possible for him to detect that the accident airplane was on the wrong runway if he had been looking out the tower cab window. ...
The concurrent radar and tower tasks that required the controller to divide his attention occurred during the window of opportunity when the controller could have, but did not, notice that the airplane was stopped short of runway 26.
After the controller transferred control of American Eagle flight 882 to the Indianapolis ARTCC, he did not have any further active radar duties. However, after the transfer, the controller performed an administrative task—the traffic count—instead of monitoring the departure of Comair flight 5191. The controller had turned around in the tower cab to perform this task before the start of the critical window. At that time, the airplane had not yet deviated from the issued clearances. However, at the end of the critical window, the airplane had accelerated beyond the maximum airspeed that would have allowed the airplane to remain on the available runway if the flight crew rejected the takeoff and used maximum braking.
Thus, at that point, the controller missed his final opportunity to notice the flight crew’s error in enough time to take action to prevent the accident.
https://www.ntsb.gov/investigations/...ts/AAR0705.pdf
After the accident, FAA increased staffing at LEX, hiring four additional controllers. It will be interesting to know the staffing levels at SFO at the time of this incident.