They aren't "wild assertions"; she had sources. That's enough for a story; it doesn't have to be "truth". Though if you suspect the sources were fictional, complain to the editor of the NYT, then other U.S. newspapers. Please! NYT reporters have been caught doing such things before.
Without political control subordinate officers have great freedom to interpret superiors' orders creatively. Remember, Pakistani politicians not only cannot appoint generals below COAS, more importantly they cannot remove bad apples. That means Pakistan's armed forces form an unaccountable polity of their own, with room for deception, personal agendas, alliances, back-stabbing, plots, and betrayals. Even if the COAS and ISI chief give orders, they doesn't mean they will be carried out in the intended fashion, nor can they easily remove suspect subordinates without a clear paper trail or evident chain of responsibility, lest they threaten cutting away their own support that pushed them to the top, or the effectiveness of their own command. In short, in a military oligarchy, orders may come from above, but legitimacy comes from below.