I actually agree that civilian meddling in military affairs (particularly from the Secretary of Defense) has often been disastrous. My argument was more that we need the president be able to understand the strategic questions instead of simply giving authority to local commanders. As I put it in the initial post
Despite John McCain's experience, he seems too ready to simply abdicate any strategic planning by hiding behind tactile military commanders.
The point of a president is not to simply supply a commander with what he says he needs. What if you have two commanders who both claim to need resources and you are unable to supply both? This is not a hypothetical , considering that resources have been pulled of
Afghanistan and the hunt for bin Laden and dedicated to Iraq. Say that he will give Petraeus what he needs only abdicates the strategic role a president necessarily plays.
I'm not sure how "apolitical" the military is. Generally is very conservative but surprisingly dovish (armies are generally more interested in preparing for war than fighting them). The principle I alluded to is civilian control of the military. This is important even if you do trust this institution completely.