Billy Budd is nothing if not a book rich in moral and ethical questions. One could frame an entire course on the philosophy of ethics around Captain Vere's dilemma. The main problem is an apparent disconnect between military law and moral sensibility. Billy's execution feels unjust, and one cannot help but ask whether, in this case, right and wrong are aligned with good and evil. At the same time, the narrative is carefully constructed so that it is neigh impossible to judge Captain Vere. You can disagree with him, but you can't help yourself from empathizing with him.
Though Captain Vere speaks against private conscience, by executing Billy he is actually attempting not only a legally right action, but also a morally good one.
As Billy is presented, he is so naive that he cannot be called good. Because he cannot even conceive of evil, he is an amoral character rather than a moral one.