Interestingly enough, the more senior (and experienced) civil servants that I have had the opportunity to talk to have been very careful to emphasise that the department answers to the minister.
Of course, the relationship between the civil service, ministers and the media is an unnatural, strained and stressful one -- I do not envy any of these parties, although I think that the media has the most (effective) power out of these three, given the proportion of central government activity (60-70%?) that is driven by whatever happened to be in the headlines that week.
So his "joke" might have been a sinister indication that they are sidestepping political control, or just pointing out the realities of who does the actual work.
But in a government "of the people, by the people, for the people", it is The People who have final say.
(edit: yes, I am aware that this particular incident happened in England, not the U.S....)
Watching "Battlestar Galactica", 3rd season beginning. Cylons trying to live peacefully with humans they occupied on New Caprica. "Either we increase control or we lose control" ...
Of course, the converse is generally true: the laughably incorrect explanations that "government people" always seem to come up with for "our" behavior often are the result of them interpreting events, statements, etc. through their lens- a lens informed by a completely different set of optical principles than the ones that we are used to using (to abuse the figure of speech a little bit).
In other words, when you read or hear about a "government person" doing or saying something head-deskingly stupid, the odds are very good that the statement or action made perfect sense in the context of that government person's world. It's not that they're (necessarily) stupid, or even ignorant- just that they're not living in our world, and so have dramatically different motivations, constraints, first principles, etc. etc. Their actions may be perfectly follow an internal logic- but it's not our logic, and so we have a hard time making sense of it.
And all of this goes double or triple when we're talking about military or IC people. The classified nature of their work, with its attendant organizational, cultural, technical, political, and psychological distortions, makes their "bubble" look more like a bathysphere.