In my opinion, there is no doubt that Holder knew. Watch this video and watch him say that he learned of it a few weeks before the scandal broke and yet he bragged about it in Mexico long before.
Mexico wants to indict those responsible for letting the guns walk and I don't blame them. This was an act of war arming the internal forces aligning against the Mexican people and the government of Mexico.
Click the picture below to watch the video (not embedded).
And those in charge are being promoted and moved to other parts of the country, some in positions invented just for them. While the whistleblowers are being retaliated against which is against Federal law. Of course, we already know from the voter intimidation charges against the black panthers stemming from the '08 PA billy club swinging incidents that Holder won't enforce Federal law if the accused / guilty are "his people".