The Captain still makes all the decisions. Since they commented on the fact that the runway was dark and they were aware that the long runway had previously had it's lights NOTAMed out it looks like they determined they were on the long runway because of the expected lighting conditions.
However, they would have had to miss the runway markings on the taxiway short of the runway identifying which runway they were entering, the runway marking on the takeoff end of the runway which also identified the runway they were on and the final check which might have saved them which was to reference their mag heading when they lined up for TO. I would also bet the then current lighting conditions were also mentioned in the NOTAMs they would have received for the flight. If they had read them they probably would have noted the changed runway lighting conditions.