No kidding. The US Attorneys work through th AG. FBI personnel often work with them on investigation, but they have no say in the actual prosecution or settlement terms.
But doesn't the FBI shelter the DoJ using the "no reasonable prosecutor" widget? If Comey had a hold of this investigation, maybe he would have kept it out of the DoJ altogether, and there would not be this sweetheart deal.
BTW, I'm being sarcastic.