No, it wouldn't be her who cannot make distinctions, it would be the bureaucracy itself. Earlier in her letter she refers to how higher-ups used to rewrite field reports to try to increase the chances of a prosecution, but the Moussaoui case had higher-ups editing reports to try to stifle a prosecution.
Then in footnote 5 she says the culture of the FBI has turned into "a climate of fear which has chilled aggressive FBI law enforcement action/decisions" because previous higher-ups had "their careers plummet and end" because of Ruby Ridge & Waco "which, in hindsight, turned out to be mistaken or just turned out badly".
I'm not defending the FBI's handling of Ruby Ridge or Waco, but Rowley's saying that post-Waco, higher-ups at the FBI are too gunshy to even push for a search warrant unless they're "75%-80% [sure] and sometimes even higher".
Could the pendulum swung all the way into overcaution in just 9 years?
I disagree. If she could see the distinction, then she wouldn't use Waco and Ruby Ridge as the examples. The fact that she uses them as the examples is evidence that she doesn't recognize the differences between these situations.