To be sure, there were plenty of instances in which American officials did less than they could have. Diplomats or politicians intent on preserving the relationship with Pakistan for other strategic reasons (its help in the Cold War and then the war on terror) downplayed evidence of its nuclear chicanery for fear that any revelations would undermine cooperation.
The most egregious case involved Richard Barlow, a young CIA analyst who figures prominently in all three books. Barlow defied the cautious dissembling about the Pakistani nuclear program that was the official line -- and then was run out of the CIA for calling the intelligence as he saw it. In another instance, the State Department apparently intervened to downplay the potential proliferation implications of a smuggling trial. Customs officials also repeatedly failed to ask questions that would have quickly led them to realize what Khan and his operatives were up to.
But despite such missed opportunities, what becomes clear in these books is that the United States at various points drew on most of the tools it had to influence Pakistan, and none of them had much effect on its nuclear ambitions.