I think it would be an open question as to which side ends up owning most of the military. Bases are all over the US along with national guard. The people in the military are also a pretty diverse group. In a civil war situation I don’t think it would be an automatic siding with DC.
One of the reasons the military has so many independent branches is that it would take all of them to rebel and join the opposing side in order to win. It's impossible to tell how they would side in a real internal conflict and the whole apparatus probably has to break down first before they will ever officially take sides of a force that opposes the federal government. At that point there will be total chaos and the wealthiest people can once again swoop in, amass the most powerful force and take over.
