What was the reason for military districts after the civil war?

After a conquest, it is customary for the military to administer the newly gained territories until a civilian government can be installed. The military will maintain Law and Order, until it deems it time for a peaceful civilian government to take it's place.

Example: California was won from Mexico during the Mexican War of 1846-48. California had 7 US Military Governors before obtaining statehood in 1850. California never had a US Territorial Governor.