The Union army made a point of desecrating churches and cemeteries in the South. And may I say it was with Abe's blessing. May God have mercy on their souls.
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Like Alice, I never heard of this practice before, but then Jamie who is quite knowledgeable, seems to concur.

Perhaps there was a general order that we never heard of, to the effect that: "Henceforth all Union troops in the field shall at every available opportunity desecrate all churches and cemeteries that they should happen onto, by decree of his satanic majesty, Abraham Lincoln."

Surely there were instances of such desecration, as when the Yankees burned out the church in which enemy combatants had taken refuge during the Battle of Marianna, FL on 9/27/64. Does this fall in line with what you're referring to?