I am wondering just how far this anti-Catholic reactions went? There was an extreme anti-Irish prejudice event before the war and in fact an anti-Catholic sentiment also, especially in the North. We have all seen those posters in New York city.
It is well known that Pope Pius the IX supported Jeff Davis and the concept of peaceful secession, a defensive war, and viewed Lincoln as an aggressor. This support included the exchanging of Ambassadors between the Vatican and Richmond.
Pope Pius also directed the Catholic Church priests in Europe to condeam the recruiting in their parishes of Union soldiers and according to Catholic Histories on Pope Pius this was successful, which I am sure that is a subjective opinion on their part. BUT, then again, most of the Lincoln Assination plotters, such as the Surrats, were Catholic. That little known and often covered up connection, in this understanding, may have been deeper than mearly the personal religions of individuals.
This leads me to wonder, in connection with your information, IF the keeping the Catholic Priest from the Irish Catholic Union soldiers in 1864, was not an attempt on the part of the federals to keep the Priest from following Pope Pius' directives, and from inciting those soldiers to desert?