Individuals rebel not States or Cities or islands. According to Lincoln, the Confederacy did not exist - only rebellious individuals in certain parts of the Union which was, in his mind, indissoluble.
Brave individuals fought on both sides of that conflict without doubt. There were slave owners on both sides. One side was fighting to preserve the nation and government we still enjoy and the other was doing all they could to rend that same nation apart.
Honoring those who rebelled against the United States is in my mind, dishonoring those fought for the the United States. No history is being rewritten by renaming this ship just a correction of an error that never should have been made.