I've been researching this subject. Churches of the South were under assualt almost everywhere. There were standing orders to force churches to pray for the president. The Catholic Church was especially targeted after the Pope's message for Catholics to resist supporting the war for the Union. Cemeteries were desecrated in some cases to build fortifactions, on church properties. Church valuables were stolen from the alters. I've seen the Marianna case, and there are many others.
Below is the case at Alexandria Virginia, the O.R. has more on this incident.
Alexandria Virginia Episcopalians to Abraham Lincoln, Sunday, February 09, 1862 (Report of a disturbance at their church)
From Alexandria Virginia Episcopalians to Abraham Lincoln, February 9, 1862
A scene occurred at St Paul's Church Alexandria, Virginia, on Sunday morning February 9th 1862, which has, perhaps, never had a parallel among civilized nations, certainly not in the history of this country.
The officiating minister, the Revd K. J. Stewart had gone through the morning prayer of the Episcopal Church as far as the Litany, and the prayer for the President being omitted, but without any thing in its place, and was proceeding with the Litany, when an interruption occurred of the character which the law designates as "brawling", that is the intervention of noise and tumult, by certain persons who had come into to the church with the intention of interrupting the service, should it not proceed according to their wishes.
These persons commenced the disturbance as soon as they found the prayer for the President omitted. One of them, Capt Farnsworth1 of the 8th Illinois Dragoons, who sat near the Chancel, dressed in uniform, with some five or six of the soldiers near him undertook to officiate in prayer (if prayer it can be called) by reading the prayer for the President of the United States. How far it he went in it does not appear in the confusion, but soon quitting his position as the offerer of prayer, he advanced to the altar where Mr. Stewart was kneeling and still continuing the Litany, and ordered the his arrest. Mr. Stewart was dragged from his knees by the soldiers. The ground was of this arrest Capt Farnsworth distinctly averred to the be the omission of the prayer for the President of the United States. With this averral he said, "I arrest you by the authority of the United States as a rebel and a traitor." And I, responded Mr Stewart, who by that time had advanced to the Chancel rails, to Capt. Farnsworth, summon you to answer at the Judgment seat of the King of Kings and Lord of Lords for interrupting interfering by force of arms with his ambassador while in the act of presenting the petition of his people at His Altar.
The solemnity of this appeal apparently caused the parties to fall back and pause, but soon the soldiers were ordered to seize Mr Stewart which two of them did with great violence forcing the bible and prayer book from his hands, one of them drawing his revolver; another revolver was presented to an old and venerated citizen within the chancel, when the officer ordered the soldier not to fire: very soon a considerable number of armed soldiers appeared in the Church.
Mr Stewart refusing to yield voluntarily, was dragged by force from the Altar, and through the aisle out of the church-- He was in the surplice, which he wore through the streets, and at Col: Farnsworth's quarters, where he was taken.
Capt Farnsworth said that he went to church intending to arrest Mr. Stewart, if he should offer any prayer for the Confederate States. Near him, in the same pew sat Mr. Morton the "detective" agent of the government, who then gave orders to arrest Capt. Farnsworth to make the arrest, which was executed as above described. Mr. Morton has declared that he was acting under authority from Washington.
The scene in the church was such as may be imagined in such circumstances-- Gentlemen were indignant and excited, and ladies giving utterance to their feelings of grief and indignation, but of course no serious effort was made to prevent the arrest-- Mr. Stewart was taken away and the congregation soon dispersed--
It is proper to state that these proceedings were without the knowledge of Genl Montgomery,2 the military governor of this city, and were strongly condemned by him when they came to his knowledge. He telegraphed to Washington for instructions from the government, which, when received, were of such a nature as to lead to Mr. Stewart's release after a few hours detention.
The issues involved in the transactions thus imperfectly sketched, are too great grave to admit of comment. It will, however, be well to state that Mr. Stewart only insists upon the the rights of all ambassadors to communicate with their King untrammelled by civil or military interference; and that in no case have any of the services of this Church assumed a political aspect; no prayer has been offered, and no sentiment advanced at any time that was calculated to offend even the most sensitive critic; but public worship is interrupted, soldiers invade the Chancel, and with drawn revolvers drag the minister s of religion from its Altar, because he will not do their bidding.
The undersigned were present in the Church and testify to the facts herein stated. It may be proper also to state that, by request of the vestry and in the absence of the Rector, the Revd George A. Smith and the Revd K. J. Stewart have been officiating in St Pauls Church for several weeks past, and that Mr. Smith was in the Chancel, at the time these occurrances took place.
George A. Smith
Cassius F. Lee
Sidney G. Miller
A. H. Currie
John A. Dixon
W. H. Marbury
Townshd. D. Fendall
Albert F. E. Barsford
Edwd. C. Fletcher
Geo. H. Smoot
J. J. Wheat
W. A. Harper
Nathl. P. Brush
P. A. Clagett
Thomas W. Swann