I am glad to to see President Obama exercising his authority over the military. Even though our society regular treats military leaders as dispassionate experts, it is worth noting that military leaders always have an agenda.
I am reminded of a story about how Franklin Roosevelt exercised his authority as commander in chief. During the early months of World War II, Roosevelt was embroiled in a debate with his top military commanders. President Roosevelt agreed with Winston Churchill and the British military that there should be an invasion of North Africa. The American military did not want to invade North Africa. Army generals wanted to invade Europe directly and they wanted to invade as soon as they could. Navy Admirals did not want to invade North Africa because they wanted the resources allocated for North Africa to be sent to fight Japan in the Pacific Theatre.
When the allied governments announced their intentions to invade North Africa, American generals and admirals got together and said that they could not support the plan and all the the resources should be diverted to the Pacific. Roosevelt called their bluff and told them to have a detailed plan to him the next morning. Since the military did not have a plan ready, the plan they produced was not very good. Roosevelt rejected the plan and ordered the military to go along with the invasion of North Africa.
Roosevelt knew what I hope Obama is learning and that is the military's agenda does not always coincide with what the President was elected to do.