To play devil's advocate here: from the average Pakistani's point of view, the US must have known a lot of this from day one (or before day one). If they let it go on, either they are incompetent or involved.....ISI is not the only people with a credibility problem here.
I dont mean to imply that this is some vast conspiracy. I personally think things are generally what they appear to be, not some deep dark conspiracy by the elders of Zion. But I must say that in this case "as they appear to be" includes the US turning a blind eye to many activities that were not very hidden, so one can be excused for thinking that motivations may not have been pure as driven snow OR incompetence may be greater than we imagined.