Your correct. The list of Churches is almost endless, some discribe both Confederate and Union occupiers but the Union is almost alone in converted churches into stables. Both sides are credited with turning them into hospitals or headquarters.
First Presbyterian Church, Holly Springs (built in 1860) designated as a Mississippi landmark. It was built in a Romanesque style and not completed when the war began. Federal troops occupied the church and turned the basement into a horse stable in 1862. After the war, the northern people paid for the completion of the church and donated the Bohemian windows. [The South Reporter, Nov 30, 2000]
THE HISTORY OF ST. PAUL'S
AND ITS MAGNIFICENT ASCENSION WINDOW
During the Civil War when occupied New Orleans was under the military rule of Union Gen. Benjamin Butler, Major George C. Strong of the general's staff attended services at St. Paul's and noted that the Rev. Charles Goodrich omitted the Book of Common Prayer's prayer for the President of the United States. Strong stood up and angrily ordered that the service end immediately, saying "This house will be shut within ten minutes." Rev. Goodrich explained that in an effort to remain neutral he did not offer a prayer for either the President of the United States or for the President of the Confederate States. When told of this incident, General Butler retaliated by keeping the church closed, sending Rev. Goodrich to prison in New York and using the marble-floored church as a place to stable the Union troops' horses.
http://www.stpaulschurchno.org/spc_history_2.htm
Pohick Church, Virginia
...the Civil War brought new devastation when occupying Union forces stripped the building’s interior for souvenirs of "Washington's Church" and used its worship space as a stable. Soldiers scrawled their names on the the inside walls, carved graffiti onto the doorposts, and pockmarked the exterior with bullet holes. The interior damage can be seen from an 1862 Matthew Brady photo, while the outside markings can still be viewed today.
http://www.pohick.org/history.html
Holy Trinity Episcopal Church, Nashville.
During the Union occupation of Nashville during the Civil War, Federal troops used the church to store powder and stable horses and damaged much of the interior furnishings. The church was restored by the turn of the century.
http://www.bonps.org/tour/holytrinity.htm
Downtown Presbyterian Church Nashville
This church was one of many buildings used as hospitals during the Union occupation of the city during the Civil War. It was designated Hospital No. 8 and housed 206 beds.
St. Mary's Cathedral Nashville
The oldest surviving church in Nashville, St. Mary's was used as a military hospital during the War Between the States.
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I'll stop here, my list goes on and on.
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David Upton