An Awkward Question for Robert Gates: Has the Deep State Taken Over?

What little I've read of Robert Gates's memoir is praiseworthy: Unlike so many public figures, who are shallow and self-serving in their indelible statements to history, the former secretary of defense appears to have delivered a forthright manuscript infused with moral criticism of the ruling-class tribe to which he belonged. His critiques are an important addition to public discourse, as you'd desire from a man no longer charged with governing, managing, or administering.  

One passage struck me as more troubling and revealing than its author perhaps realizes. It concerns the Afghanistan policy review in 2009 and General Stanley McChrystal's surprise request for a substantial escalation of U.S. forces. The request "surprised the White House (and me) and provoked a debate that the White House didn't want," Gates wrote. "I think Obama and his advisers were incensed that the Department of Defense—specifically the uniformed military—had taken control of the policy process from them and threatened to run away with it." 

Civilian control of U.S. foreign policy is rather important. So I can't help but marvel at the casual manner in which this former secretary of defense observes that the uniformed military did take control of the policy process with regard to Afghanistan, and implies that they had the capacity to "run away with" the policy process. 

If true, isn't that cause for alarm? When insiders seem to take it for granted that the president isn't quite in charge, when even Obama himself frames his relationship with the NSA as one where he proposes that they rein themselves in, rather than ordering them to act within constraints he sets, what are those of us on the outside to think? A while back, Mike Lofgren, a longtime congressional aide, expressed alarm at the power of the "Deep State," especially in the realm of national security:

Clearly there is government, and then there is government. The former is the tip of the iceberg that the public who watches C-SPAN sees daily and which is theoretically controllable via elections. The subsurface part is the Deep State, which operates on its own compass heading regardless of who is formally in power. The Deep State is a hybrid of national security and law enforcement agencies, key nodes of the judiciary (like FISC, the Eastern District of Virginia, and the Southern District of Manhattan); cleared contractors, Silicon Valley (whose cooperation is critical), and Wall Street.

The excerpt of Gates's memoir suggests that the Deep State's power, and the attendant weakness of the elected officials meant to control U.S. policy, is in fact a problem. And I wonder if Gates would be willing to address the matter. Even if I've read too much into the particular excerpt I've cited, what are his thoughts on the subject? As the nation ponders whether or not to reform the surveillance state, how constrained is Obama by the Deep State? With regard to Iraq, Afghanistan, and counterterrorism efforts, is it Gates's assessment that the uniformed military is capable of running away with the policy process? If so, what reforms would he suggest to ensure full control by accountable, elected civilians?

Alternatively, why is he comfortable with the Deep State?

An answer would be a real service to members of the public puzzling through these questions.

And who knows, it might even sell some books.