The US military was very much opposed to the confederate succession, so much so that they refused to hand over union/federal property, which started the civil war to begin with.

https://en.wikipedia.org/wiki/Battle_of_Fort_Sumter

This is a good point. After the conclusion of the war, 10 former Confederate states were placed under military rule. However, I believe that happened under the command of civilian leaders. Whether or not they had legitimate authority to do so is a different debate, but I don't think it was the military acting of its own accord.