Middle Passage should be viewed through one crucial detail: The ship is named "The Republic," which is an illusion to Plato's masterpiece, The Republic, in which he explains a basic metaphor: Plato uses a group of people to represent the soul. For the boat to be called "The Republic" is to say that the boat will represent a single human soul coming to its enlightenment.
Calhoun is a freed slave, but that doesn't mean he is completely autonomous. He still finds himself unable to control his fate until finally, he tries to speak reasonably to the slaves who are destroying the ship, explaining that if they continue, they will die. This represents a person working through their deep anger and resent, because Calhoun is a former slave; he literally does commiserate with their plight, but at the same time, he has the foresight to understand that if they only obey their emotions, they will die. Therefore, the tribal slave overthrow represents the id's thirst for justice and vengeance, and Calhoun represents the autonomy of the superego.
At the end of the story, the ship goes down, which is a sign of death (especially if the boat sinking is called "The Republic." So, that's the story's way of analyzing Calhoun's honor. He wins back Isadora, this time of his own free will, and they return to his freedom in America. That means that he has accomplished heroism, and his boon is that he has a wife and has his freedom returned to him, and his debt? Cancelled because Calhoun knows that Zeringue is doing illegal business with slave traders. He frees a slave and goes home. This is ultimately a picture of enlightenment.