The Permanent State vs. Democratic Government

This WSJ piece nicely illustrates the difference between the permanent apparatus of the state and the impermanent apparatus of elected government. It also illustrates nicely the problem of legitimacy in the context of a large state. The legitimacy of government coercion and redistribution, according to most contemporary liberal theorists, flows from decisions having passed through fair democratic procedures. But much de facto government comes from the unelected state, even under normal conditions. 

Much of the planning required to give out the funds is being done by career bureaucrats, because top political appointees at many agencies have yet to be nominated, much less confirmed.
At the Interior Department, an eight-person task force is mostly made up of career employees who have been named acting bureau chiefs.
Longtime employees also have been running the show at the Commerce Department, which remains without a secretary after the Obama administration's first two candidates dropped out, and the third, former Washington Gov. Gary Locke, awaits confirmation. It took a week for the agency to provide any information about its stimulus plans. The agency has almost $8 billion to give out, including $3.9 billion for broadband grants.

All the so-called liberal democracies have a permanent civil service or bureacracy. I don't see how they could function without them. But I also don't understand how this fits into contemporary liberal accounts of the democratic legitimacy. Is this a problem?
[Note: Just in case… let me say that is a post about political theory, not anything about the Obama government in particular.]