Finding yesterday’s Washington Post Outlook section as ruefully unsatisfying as ever, I nearly missed the quite substantive charges leveled in commentary by former Bush official Thomas A. Schweich — but I’m glad I didn’t — it’s a conversation we need desperately to have, but probably won’t, in 2009.

Schweich, who served under Bush as ambassador for counter-narcotics in Afghanistan and deputy assistant secretary of state for international law enforcement affairs, starts out quickly with this marker:

We no longer have a civilian-led government. It is hard for a lifelong Republican and son of a retired Air Force colonel to say this, but the most unnerving legacy of the Bush administration is the encroachment of the Department of Defense into a striking number of aspects of civilian government. Our Constitution is at risk.

President-elect Barack Obama‘s selections of James L. Jones, a retired four-star Marine general, to be his national security adviser and, it appears, retired Navy Adm. Dennis C. Blair to be his director of national intelligence present the incoming administration with an important opportunity — and a major risk. These appointments could pave the way for these respected military officers to reverse the current trend of Pentagon encroachment upon civilian government functions, or they could complete the silent military coup d’etat that has been steadily gaining ground below the radar screen of most Americans and the media.

Schweich goes on to underscore what is hardly a secret in Washington bureaucratic circles, but is not so often used so effectively in charges of military mission creep:

While serving the State Department in several senior capacities over the past four years, I witnessed firsthand the quiet, de facto military takeover of much of the U.S. government. The first assault on civilian government occurred in faraway places — Iraq and Afghanistan — and was, in theory, justified by the exigencies of war.

The White House, which basically let the Defense Department call the budgetary shots, vastly underfunded efforts by the State Department, the Justice Department and the U.S. Agency for International Development to train civilian police forces, build functioning judicial systems and provide basic development services to those war-torn countries. (snip)

Until this year, the State Department received an average of about $40 million a year for rule-of-law programs in Afghanistan, according to the department’s Bureau of International Narcotics and Law Enforcement Affairs — in stark contrast to the billions that the Pentagon got to train the Afghan army. Under then-Defense Secretary Donald H. Rumsfeld, the Defense Department failed to provide even basic security for the meager force of civilian police mentors, rule-of-law advisers and aid workers from other U.S. agencies operating in Afghanistan and Iraq, driving policymakers to turn to such contracting firms as Blackwater Worldwide. After having set the rest of the U.S. government up for failure, military authorities then declared that the other agencies’ unsuccessful police-training efforts required military leadership and took them over — after brutal interagency battles at the White House.

But it is when Schweich assesses the domestic creep that things really start getting interesting. He talks about the Pentagon, led by former SecDef Donald Rumsfeld and VP Dick Cheney, populating and intimidating civilian national security and foreign policy agencies — the National Security Council, State Department and USAID in particular, which in a climate of war and an executive branch seeking new frontiers of power, were exposed and exploited over time:

As military officers sought to take over the role played by civilian development experts abroad, Pentagon bureaucrats quietly populated the National Security Council and the State Department with their own personnel (some civilians, some consultants, some retired officers, some officers on “detail” from the Pentagon) to ensure that the Defense Department could keep an eye on its rival agencies. Vice President Cheney, himself a former secretary of defense, and his good friend Rumsfeld ensured the success of this seeding effort by some fairly forceful means. At least twice, I saw Cheney staffers show up unannounced at State Department meetings, and I heard other State Department officials grumble about this habit. The Rumsfeld officials could play hardball, sometimes even leaking to the press the results of classified meetings that did not go their way in order to get the decisions reversed. After I got wind of the Pentagon’s dislike for the approved interagency anti-drug strategy for Afghanistan, details of the plan quickly wound up in the hands of foreign countries sympathetic to the Pentagon view. I’ve heard other, similarly troubling stories about leaks of classified information to the press.

Many of Cheney’s and Rumsfeld’s cronies still work at the Pentagon and elsewhere. Rumsfeld’s successor, Robert M. Gates, has spoken of increasing America’s “soft power,” its ability to attract others by our example, culture and values, but thus far, this push to reestablish civilian leadership has been largely talk and little action. Gates is clearly sincere about chipping away at the military’s expanding role, but many of his subordinates are not.

Schweich points to DoD-led domestic surveillance, authority over terror suspects and a more recent plan to deploy 20,000 Army soldiers on American soil for “homeland security” efforts as further manifestations of the creep. And without some sort of reversal by the new administration, it is unlikely it will stop. To be sure, prominent civilian officials like Steven Hadley have hardly wrapped themselves in glory, nor did leadership at Foggy Bottom under Condoleezza Rice give that agency a fighting chance, but Schweich recognizes that true “change” can only happen by getting rid of the Bush baggage at the lower, and less obvious levels, and putting the breaks on a DoD march on Washington (which by the way, hasn’t started off too well considering Obama’s recent intelligence and national security appointments):

Above all, he should let his appointees with military backgrounds know swiftly and firmly that, under the Constitution, he is their commander, and that he will not tolerate the well-rehearsed lip service that the military gave to civilian agencies and even President Bush over the past four years …In short, he should retake the government before it devours him and us — and return civilian-led government to the people of the United States.

Schweich will be taking questions online this morning at 11 a.m. ET at www.washingtonpost.com/liveonline