Welcome, Sappeur
I don't know enough about the inner workings of DoD to say whether the current structure is wise or not, but Andy Bochman & Dan Nolan run a website which is very thorough in examining DoD's approach to energy use (in terms of departmental organization, mandates, budgets, implementation, etc... just in case you aren't aware of it):
http://www.dodenergy.blogspot.com/

Bill,
I agree.
Again, DoD is a leader in both research and in application when it comes to energy conservation. At the 2010 ASPO conference, RADM Larry Rice said that he felt DoD was doing its part (and mentioned several efforts by USN) and that the civilian sector needs to get serious/on board as well.