Poor leadership does not justify a soldier deserting then or now. Leaders come and leaders go. Soldiers knew the rules. A soldier standing before a court-martial could not use bad leadership as a defense.
What I look at is how soldiers were reported by their leadership in the company muster rolls. You cannot argue with the record. The company leadership was there, knew the families, the communities, and knew the people.
In the study of War Between the States history one must be objective and take off the idealized lenses many put on themselves when they look back at a very painful time period in our history. We Southrons are particularly bad about doing this. The South was not a big happy family as is often portrayed today. This is particularly true in the entire Appalachia region. The time of "enlistment" and circumstances is particularly important to analyze. Conscription began in April 1862. The threat of conscription began at least sixty days prior to this. Soldiers that "enlisted" during this time or after were under the specter of conscription.
Soldiers that "galvanized," that is they joined U.S. Volunteer regiments from Federal prisons and went out west and soldiers that deserted and joined regiments that fought within the same theater of war that they were captured in are two different classes of people. For discussions on "galvanized" soldiers you will want to read "The Galvanized Yankees" by Dee Brown.
One can begin making judgements on why soldiers deserted if you look at the circumstances and pattern analysis. Let me provide you with the concluding paragraph from my Master's Thesis, "Free or Dead: Loyalty, Desertion, and Will in the 39th Georgia Volunteer Infantry Regiment,"
"The story of desertion in the 39th Georgia is the story of the twists and turns of both United States and Confederate States politics and of the mismanagement of soldiers and material resources by Pemberton and Bragg's leadership. The foremost event taht produced desertions in the 39th Georgia was the siege of Vicksburg and its aftermath. It is evident from the number of men failing to return to duty when called back to parole camps that many had had enough of the Confederate cause. The next event that resulted in the second wave of desertions was the maneuvering and aftermath of the Chattanooga Campaign. This, coupled with the geographic proximity of the soldiers to their homes in the fall of 1863 and winter of 1864, allowed for easy access for them to go home. Why did the soldiers desert? Unless they left a historical record similar to that of Robert Magill we will never know the individual reasons, reasoning, or cognitive struggle the individual soldier went through before he abandoned the ranks and left comrades and combat. One can only analyze the situations and circumstances under which they lived to determine why they made the choices and decisions that led to the events discussed in this paper."
Below are several books or articles you may want to read.
Henderson, William Darryl. Cohesion: The Human Element in Combat. Washington D.C.: National Defense University Press, 1985.
Lincoln, Abraham. The Proclamation of Amnesty and Reconstruction, (College Park, Maryland: Freedmen & Southern Society Project, University of Maryland, accessed June 11, 2009); available from http://www.history.umd.edu/Freedmen/procamn.htm; Internet.
Lonn, Ella. Desertion during the Civil War. Lincoln and London: University of Nebraska
Press, 1998. Reprint, Gloucester, MA: Peter Smith, 1966.
MacCoun, Robert J., Elizabeth Kier, and Aaron Belkin. “Does Social Cohesion Determine Motivation in Combat? An Old Question with an Old Answer.” Armed Forces & Society 32, no 4 (July 2006): 646-654.
U.S. Army Field Manual 22-51, Leader’s Manual for Combat Stress Control. Washington,
D.C.: Headquarters, Department of the Army, 29 September 1994.
Weitz, Mark A. A Higher Duty: Desertion among Georgia Troops during the Civil War. University of Nebraska Press: Lincoln, 2000. I don't agree with everything that Wietz states but it is a good starting point.
Enjoy.
Respectfully,
Gerald D. Hodge, Jr.
M.A. Military History - Civil War Concentration
War Between the States Historian
Historian: 39th Georgia Volunteer Infantry Regiment