That's easy to check because chaplains are commissioned staff officers.
Many ministers enlisted to care for the spiritual needs in the Confederate army, but discovered the rigors of military life to be more than they could endure. For what it's worth, General Thomas J. ("Stonewall") Jackson wanted a full complement of chaplains in his command (one per regiment), but insisted that every chaplain be prepared for life in the field as one of the soldiers.
In the absence of a regularly appointed and commissioned chaplain, many officers and enlisted men acted in that capacity. Unfortunately military records will not help identify anyone who served as an acting chaplain.