Huh? You got your order backwards re: the pentagon. Its not the politicians saying what the generals want them to say, its the generals saying what the politicians want them to say... usually. Open disagreement tends to be a sign of retiring from higher military posts.
The US military has, since close to its inception, been getting the final order from civilians, i.e. Congress and the president. This is enshrined in the constitution, and military folks tend to take their role in the constitution alot more seriously than most (dead seriously in fact, as this is part of their vows), as well as tending to lean right in the spectrum of politics.
That is not to say A former general can't be the civilian head, and Presidents actually tend to have a military history, but at the end of the day it is the president and congress that order the military, as it has always been in the US.