For a perspective on conditions in Jackson County, pick up the memoirs of Milus E. Johnston.
http://openlibrary.org/works/OL4327189W/The_sword_of_Bushwhacker_Johnston

My copy was printed by the Flint River Press in 1992. Johnston writes on pages 16-17, "When the old flag was cut down at Montgomery and Alabama went out of the Union, many a brave heart was moved, and many an eye was filled with tears." Johnston mentions praying that secession would not come to pass, and as a minister of the gospel he had no intention of being involved in military service for either side.

Federal occupation of the Tennessee Valley during the summer of 1862 and their return in the summer of 1863 changed the feelings of many residents who were inclined to remain neutral. Johnston's own treatment by Federal officers "rubbed a few drops of secession blood into our consitution." The hostility of Federal troops during the occupation, plus the activities of Union partisans like Ben Harris and John Dickey, pressed many in this mountainous country into Confederate ranks. As Johnston declared in late 1863, "Boys, I have come to the conclusion that God never yet made a man to be slobbered on by dogs!" "Bushwhacker" Johnston became a Confederate officer, eventually leading a battalion of men from Alabama and Tennessee, almost entirely recruited behind enemy lines.

A remarkable parallel may be drawn to partisan bands which organized in parts of Europe during WWII. Harsh treatment of civilians led directly to resistance, just as it did in Jackson County. People in each occupied country elected to assist the German military, even enrolling in military and paramilitary commands whose primary purpose was to surpress partisans. When the war ended, those who survived the war were subject to reprisals by their neighbors.

People who decide to aide invaders have always fascinated me. I spent well over a year preparing a master's thesis on different groups of people within Belgium who supported Germany and enrolled in their own units of the German army. The loyalists who aided the British during the American Revolution suffered the same kind of reprisals as these people did after the war. Loyalists in Jackson County happened to be on the winning side, unlike the other two groups mentioned. They received preferential treatment during the Federal military occupation of Alabama, which lasted several years after Appomattox.

Johnston's narrative describes the conversion of a peaceful Union supporter into a Confederate partisan. For anyone interested in Jackson County during the war, it makes interesting reading.