The volume DICTIONARY OF TRANSPORTS AND COMBATANT VESSELS, STEAM AND SAIL, EMPLOYED BY THE UNION ARMY, 1861-1868, compiled by Charles Dana Gibson and E. Kay Gibson, indicates, on page 24, that there were five vessels, employed by the Union Army (NOT the Union Navy), which carried the name ATLANTA. The steamer ATLANTA, of 1054 tons was chartered between November 23, 1864 to July 14, 1865 - "utilized as troopship from Chesapeake to Wilmington, NC, in Feb 1865."
The DICTIONARY OF AMERICAN NAVAL FIGHTING SHIPS (which names, as far as I know, ALL ships commissioned in the United States Navy, up to publication of those volumes, and which ships carry the appendage "USS") has a lengthy description of the first USS ATLANTA (formerly the CSS ATLANTA), and the last paragraph on this particular vessel states: "After the collapse of the Confederacy, ATLANTA steamed north to Philadelphia where she was decommissioned on 21 June 1865. She was sold at auction at the Philadelphia Navy Yard to Sam Ward on May 4 1869. No record of her subsequent fate has been found."
Hope this helps somewhat.