The consequences of cutting high ranking bureaucrats out of chain of command or information loop.

The managerial state has its rules and penalties for violating them. One of the most important is that the bureaucratic chain of command is inviolate no matter how slow and inefficient it is even to the point where it causes failure. Circumventing the chain of command especially if it brings success makes this managerial crime far worse because it reveals the inherent flaws of the system and shows how unnecessary many of the ranking apparatchiks in it are. This must never be permitted and miscreants must be harshly punished otherwise the plebs will catch on to what an overgrown, inefficient and unnecessary failure the managerial state really is. People in power usually will not give it up of their own volition and the greater their power, the more they will fight tooth and nail to keep it. Therefore any threat to that power must be ruthlessly dispatched at once.

Submitted for your consideration this article from PJ Media: Make No Mistake: The Mueller Investigation Was All About Flynn (March 26, 2019)

Michael Ledeen makes the case that General Flynn's circumvention of bureaucrats in the Pentagon and Intel community to get intelligence out to soldiers in the fields of Iraq and Afghanistan as quickly as possible where it would do the most good. In our managerial bureaucracy, success is not an option and Flynn's marginalization of his ranking lieges (and making them look bad in the process) was an unforgivable crime requiring the Mueller probe to wreak vengeance.

I agree with Ledeen that Flynn was a marked man even before the Trump Presidential campaign and when Flynn joined Trump's campaign, the ruling class would see it as a veritable nest of vipers. But in the light of the Steele dossiers prominence in obtaining the FISA warrants, it would be more likely the ruling class saw it as an opportunity to kill two birds with one stone that gives cover for the real reason Flynn was targeted. There are many reasons for the ruling class establishment to attack Trump and certainly the Flynn affair is one of them, perhaps a significant one, but arguably not the primary reason. Still in all, a good article and well worth the read.