Even in such a case, the AG should be free to ignore the recommendation and say "sure, we've got enough evidence, but we're not going to pursue it". For example, if the charge is minor enough, or if the optics of it look bad, or the person in question were already being prosecuted by a different office, they could tell the FBI Director they weren't going to bother, and then go hold a press conference to explain why (so that the FBI Director doesn't beat you to the press to say "we've got them dead to rights and they won't prosecute for [X] reasons!").