Germans used warships and converted merchant ships as surface commerce raiders during WWI. They even used a 3 masted sailing ship for one. The Seeadler captured 15 ships before grounding on a reef ended her career. They used warships such as Graf Spee and converted merchant ships such as Atlantis during the WWII. By the time WWII rolled around, the controversy over using submarines to interdict enemy shipping had all but disappeared. The CSS Alabama was well within it rights to attack and sink U.S. flagged commercial vessels.
Only if you accept the premise that the CSA constituted a legitimate separate nation. If you maintain the fiction that they were merely a "rebel" section of a single nation, than any activity by any ship under their control constitutes mere criminal acts.
As I have said several times before. The "condition" of the CSA is in a quantum state of superposition, being both legitimately a separate nation, and simultaneously a rebelled section of a single nation, depending on the need of the winning government to paint it as one thing or the other.
It's status is completely subjected to the instantaneous needs of the victor, and could be changed as necessary to fit whatever rationalization argument they wished to put forth.