My take on the Black Ship:
I think the Black Ship was actually a metaphor for Rorschach's view of the world. In the comic, the sailor performs gruesome deeds (making the human raft, murder, etc) in order to do what he thinks is right (save his family), but at the end, it's revealed that he's doomed himself, and he swims out to take his place on the Black Ship.
Moral being, the ends do not justify the means. If you do evil, you'll become evil.
And that's Rorschach's view. Ozymandias, and all the others, are...well, not comfortable, but accepting of an idea that'll kill millions to save billions. Rorschach isn't, because, to him, evil is evil, and there are lines that can't be crossed.
He forces Joe(?) to kill him, because he can't live with either alternative -- either he lets them get away with it (which means he has given in to evil), or he exposes the plot (in which not only will the millions have died in vain, but the Earth will be up for destruction again).
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