Hi Steve,
In the end, it was all over, and everyone knew it. Since it was a military ship, it was surrendered. Although it never fired a shot in anger, it did lay mines in the Red River at Alexandria, eventually sinking the Union ironclad Eastport. A turncoat? Absolutely not. Carter held on until there was nothing else to hold on to. In my book, he was a very noble man, "True to the Cause".
Jonathan Carter was in the first class of the Naval School in 1845 (later to become the U.S. Naval Academy), being pulled out on official duty several times before finishing. He was with Admiral Perry during Perry's trip to Japan in the 1850's, but resigned his commission after the beginning of the war, and "went south".
After the War, he married and moved across the Red River, settling in Bossier Parish, and working a plantation he bought. The Red River, which rarely provided him water levels to operate in during the War, flooded many times afterward, ruining his crops. He eventually moved to South Carolina, where he died in the early 1880's.