The Real Villian
Has anyone else noticed this story's real villian? Claggart was accusing Billy of mutiny, and he ends up striking Claggart over what was admittedly a trumped up charge by the Master-at-Arms. Here is the irony. According to the Mutiny Act, the law governing the Royal Navy at the time, mutiny could be punished at the discretion of the court-martial. This could be anything from a warning to the yardarm. On the other hand, the court had no discretion when it came to striking an officer.
This was a mandatory death sentence.
So, Claggart by hitting Billy with a charge having a potential death sentence, provokes him into an act that had a mandatory death sentence, insures that the object of his hatred will be hanged.
I would suggest that given the totality of his circumstances, (the fact that they were at war with the French, the fact that the average sailor in the Royal Navy at the time was likely to be an impressed man, or an outright criminal given the choice between jail or service aboard the King's ship, or a debtor, as opposed to someone who wished to 'join the Navy and see the world', or who was motivated by patrotism) Vere felt that he had to act decisvely or the crew's performance in an emergency would possibly be compromised.
Since the law was the law, Vere seemed to feel that there was no point in waiting for the admiral, since according to the Act, even his hands would be tied. In addition, with the crew that he had, any sign of weakness on Vere's part could be disastrous.
In short, Vere is shown to be a man faced with an awful choice. If he follows the law, then he in effect, abandons his conscience. If he follows his conscience, then he breaks the law, and is also faced with possible mutiny.
And at the time, the Royal Navy was under a greater threat of mutiny that normal, as two well-publicized mutinies had had just taken place, one at the Spithead in Hampshire and the other ocurred at the Nore near the head of the Thames.
So, in order to maintain what he sees as the necessary discipline, he has to show that he is willing to sacrifice anyone, even the most innocent, to achieve this. The law leaves him no choice in any event.
This, then is the real villian: the Mutiny Act. Given the circumstances, Vere makes the only choice that he can make and Melville does not condemn him.
What Melville does condemn is the harsh and merciless Act under which Vere was operating.