Did you know that several spies defeated polygraphs multiple times? If you don't believe what you are doing is wrong with how is a polygraph going to pick it up?
Conflicting views on Ames "defeating " the polygraph as in he was buttering up the examiner who gave him the benefit of the doubt when descrepencies were noted. They were there during one of his periodics, but were interpreted incorrectly when they looked back and reviewed the records.
Are polygraphs foolproof? No, but they've become the norm for other agencies to place people in positions of trust, DoD may want to follow suit. Granted the headlines would be terrible when a large portion of individuals fail them over previous drug use, but sometimes you have to break a few eggs...
Hindsight is 20/20. Sometimes it's one of those "they fooled us all" and other times it's one of those "It was pretty obvious and/ or we should have screened them better." I'm guessing, given the subjects background, in this case it's going to be the latter.