I like that part in the movie.
A big element of the first film was that Gotham is worth fighting for despite the crime, because the people there are good, even with all the social conditions that breed crime. It's just that the bad people have too much power, and the desperation creates new bad people.
The film was dark, but it would had been a bit too cynical if the ferries actually tried to blow each other up. The Joker would win too much.
It would also lessen the impact of Batman "becoming the villain" to give people the "hero they deserve" (Dent). Because they wouldn't actually deserve it.