the desertions happened MAINLY because it was obvious to many that the war was over in all but name.
had there been mass executions by the damnyankees, the number of bluebellies killed from ambush would have been MASSIVE, especially if a leader like 'ole Nate Forrest called for a guerrilla war.
free dixie,sw
Earlier guerrilla activity by confederates, especially in the Western theater and the trans-Mississippi, had done much to alienate the formerly sympathetic population. Many of the confederate partisan rangers were simply criminals who stole from friend and foe alike.