CIA versus the Pentagon: Who Does It Better?

The arguments made in the New York Times today by Daniel Benjamin and Steven Simon, former Clinton NSC officials, about the Pentagon's bureaucratic incapacity to plan and execute small-scale anti-terrorist operations is persuasive enough. As the two of them note, despite the fact that the Special Operations Command budget has ballooned since 9/11, DOD too often succumbs to risk aversion when tasked with devising plans to take out al-Qaeda leaders and other enemies. Speaking of the military's superb unconventional forces, like the Navy Seals and Delta Force, Benjamin and Simon conclude that

...fear of failure and casualties has meant they are seldom, if ever, deployed for such counterterrorism operations. In theory, the best place in the government for small-scale missions to be planned and executed is the Pentagon, because snatch or kill teams should be plugged into a larger military support team. The reality, unfortunately, is that they can't be plugged in without being bogged down.

That's a fair diagnosis of a serious ailment. But is their prescribed cure -- turn over such operations to the CIA -- any better than the disease? Granted, a small CIA paramilitary force performed admirably and nimbly in the early stages of the war against the Taliban. But is militarizing the CIA any better an idea than the reverse -- Rumsfeld's deservedly-maligned attempt to bypass Langley by building his own intelligence apparatus at the Pentagon? I tend to think not, but perhaps there are further arguments that could persuade me. Any experts out there care to weigh in?