Of course - the goodness of military men and women does not evaporate over night if there is a terrible person occupying the White House. However, when I served in the Pentagon during the Clinton Administration, I witnessed a politicalization of the military that was influenced by that same White House.
For one thing, the political appointees who were high ranking GS or SES had tremendous influence over the military, who was promoted, what policy came about, how meetings ended, and who was "favored."
Moreover, I saw first hand Generals kowtow and waffle in their decisions because they knew it would rub their political superiors the "wrong" way. I would say 90% of Generals and Admirals should be Generals and Admirals, and the system works pretty well - but even those 90% have a political streak (or they would not be Generals and Admirals).
Lastly, there are flag officers who have serious "issues" who feel the gates are unlocked when a liberal Commander in Chief is in power, and go hog wild. When they feel they can get away with it, they feel no one can stop them (and they are correct).
I was in the Pentagon when this person was running wild in the corridors.
You want to talk about a train wreck. Plus, everyone knew she was a Hillary favorite. Another woman SES knew it too - and saw what she got away with - so it sort of multiplied.
I am afraid we will see this problem again with an Obama Administration. The military is made up of human beings. Some senior leaders (both officer and enlisted) are fantastic and their character will shine through no matter what. Then again, we have some really bad apples who will cause mayhem and wreckage. They are human beings and sinners. When the top guy in charge is someone like BJ Clinton or Obama, watch out.