As you know Religion orders are made up of people and religion aside they frequently have opinions on politics. Ministers, Priests, Nuns etc frequently had an opinion during the American Civil War. Some left their orders to fight, others merely carried on with their work but expressed themselves. I came across this interesting side note of Convent lore in "Marylanders In The Confederacy" by Daniel D. Hartzler.
The archives for the Visitation Convent in Georgetown where there were eighty-three nuns during this period are blank, except for a single entry of a sister who wrote, "there was a great deal of tension in the community of the Convent because sisters from both sides were living together. The strains that these woman endured in such constricted circumstances was severe. Roughly half of the sisters were born in Ireland and may not have taken sides. The remaining residents were equally divided between the North and the South. All agreed that whenever a foot-weary soldier came to the door for refreshments or water, he would be cared for. So according to convent lore they worked out this solution: Nuns of Southern sympathy would feed Johnny Reb, and Northern nuns would take care of Billy Yanks. whenever all were together, it was understood they would never discuss the War."