As a dual to the previous post about why so few mavericks-that-get-the-job-done are pulled out of retirement, it's worth looking at why so seldomly we have events similar to e.g. (some part of) the CIA engaging in a plot to assassinate US government officials who have policies they disagree with, as seen in the first season of Madam Secretary, for instance.
We know it's silly TV stuff, obviously, but why doesn't stuff like that happen? Partly because inaction is by far the default behavior, partly because terrorism takes a lot of effort and gets poor results almost always, and partly because only people who generally support an organization as it exists choose to join.
But there are also structural things limiting defiance in big hierarchies.
In these organizations (approximately) everybody has a boss, and the way you get resources from a boss is by impressing them. In an environment like that, you'd anticipate few secrets kept from the top, and certainly almost no ability to coordinate resources against them. The people who have resources use them to impress superiors – that is the singularly defining characteristic of people in the middle layers of a bureaucracy. Using resources for something you'd be admonished for is something an individual can choose, but if you would do that, it's unlikely you'd get promoted, and you'll not end up having resources later.
In these cases, the incentives build a culture around themselves: do the very basic thing you've been told to do, whatever the purpose of your organization is. If people don't, they'll never get the approval of their immediate superior – that's the mechanism by which delay is introduced, and e.g. people at NOAA will report weather accurately instead of bolstering Trump's lies, when cabinet members show no such resolve.