Bureaucracies have inherent flaws - it takes massive numbers of people to run an operation as vast as the U.S. government, and some of those people may put their personal desires ahead of duty to their job. That said, I have a friend who has worked at a high level in the Canadian public service. This person has repeatedly conveyed to me the seriousness with which staff take the concept of offering unbiased policy information to politicians. To be sure, maintaining a high degree of professionalism in an environment of hostility like that of the Harper administration can take a toll on morale, but that's the job.

As for the fears of entrenched civil servants resisting Trump, it's a unique and complicated issue. The U.S. military has refused to act on a Trump tweet declaring trans members ineligible for military service of any kind. Is that a deep state action or a responsible reliance on proper channels? 

I take some comfort in rational, informed civil servants soldiering on.