Yes and no. Melville's concern in this novel is actually much greater than merely presenting the reader with a theme that points out the futility of war or how negative it is, although this is definitely a subtheme in the text. What is much more important to focus on is the way in which the text presents society as an unstoppable force that overpowers the individual will of its citizens. Melville uses war to demonstrate this theme through the way in which Billy is forced into fighting in a war that he has no desire to be a part of. Note how the names of the two ships reinforce this message. Bellipotent, which means "the power of war," takes Billy from the Rights-of-Man, which is very obvious symbolism: society is presented as omnipotent as it forces individuals to fight in war, and through doing this it completely ignores any rights that these individuals may have. It is thus highly significant when Billy says in Chapter 1:
And good-bye to you too, old Rights-of-Man!
The name of this ship was also a pamphlet written by Thomas Paine that argued political revolution was possible if the government does not respect and protect the rights of its citizens. The way in which Billy Budd is seized against his will and forced to participate in a war that he has little interest in strongly suggests that this novel isn't necessarily anti-war so much as anti-state, or at least it is writing about the ways in which the state can have so much power that it curtails the freedom of its citizens. In theory, the state exists to guarantee its citizens freedom, which is why Paine argued in his pamphlet that under certain conditions political revolution was acceptable. It is important therefore to realise the way in which Melville is not directly attacking war, but the power of the state.