Billy Budd is a lot of things. It is a tragedy and a drama, a piece of historical fiction, a literary and philosophical work. At the center of the novel, though, is a moral dilemma. It's so clear that it's easy to put into a couple of questions: what happens when human law go exactly contrary to what seems right and good? How can intention be incorporated into a law that deals only with actions, with what happens? The narrator focuses all of his energy upon these questions, and the details of the story that he chooses to give us are supposed to shed some light on what is right in this situation and what is wrong. This can be clearly seen because the characters only emerge insofar as they are linked to the moral quandary at the heart of the story.
Now, when you think of a parable, you might think of something that has a clear lesson. Think back to the Biblical parables and usually there is one message that can be distilled from the stories that Jesus tells his disciples. In those parables, however, there is a clear moral framework: good and evil align with right and wrong, respectively. In the case of Billy Budd, the situation is much more complex. The narrator seems to yearn to portray the situation in terms of good and evil, but the problem is that it exists mainly on the plane of right and wrong. And presumably, because of a shortcoming of military law, the right is aligned with evil, the wrong with good. Everything is criss-crossed and confused, and the result is that we are not going to get one clear message, only a clear question.
As strange a parable as this may seem, the concerns of the book are primarily moral, and the hope is that by hearing and thinking about the story of Billy Budd we will develop a greater moral sense that we can then take into our own lives.