The guy is a pothead (spoken by several sources). I suspect the Army was willing to overlook some past usage but he wasn’t about to quit and they won’t overlook that fact. I’d make the judgement that he was probably a daily smoker for at least five years.
It's my understanding that Loughner's enlistment ended at MEPS. He'd have never made it that far if he had weed in his system as typically his recruiter would've already administered a urinalysis prior to sending him to MEPS. No recruiter wants to waste anyone's time by sending a "hot" recruit to MEPS. This is not to say he didn't smoke pot but when one goes to talk to a recruiter and expresses interest in starting the enlistment process, one of the first thing the recruiter does is make you pee in a cup.
My money says he failed the psychological screening as it is becoming clearer and clearer that Loughner is most likely schizophrenic. They'd have detected such issues at MEPS and quickly shown him the door.