With respect to the Union effort during the American Civil War, Cowan received credit for authoring the proposal to allow individuals drafted for military service to be excused from serving after paying a $300 commutation fee. The commutation fee was intended to keep the cost of hiring a substitute (another route available to draftees wishing to avoid service) from becoming excessive. In addition, it was intended to raise money for the Union war effort. Despite the stated intent for enacting the commutation fee, it was one of the most hated policies of the war, with members of the poor and working classes protesting that it allowed the wealthy to avoid military service at their expense.