1) The people on the civilian boat were given the choice of either having a boat of convicted felons blow up, or having a boat of convicted felons blow up AND the boat they're on whose passengers include families with young children. Wouldn't the logical and moral choice for the civilian boat be to blow up the prisoner's ship?
That's a stupid question and no, there is no other moral choice here other than not blowing the other boat.
2) If given what the Joker tells them, blowing up the other boat was the ethical thing to do, does the fact that they didn't blow up the other boat mean that they did not believe what the Joker told them about blowing up the boats himself if no one did anything? If that's the case, why does Batman and the Joker seem to think that the outcome has any bearing on their debate about whether the people on the boat are good or evil?
What you say here makes no sense... I don't even think you get the point of including this dilemma at all... you keep questioning it with irrelevant 'Ifs" that don't have a place here at all, not to mention how stupid they are. Isn't the point of this scene for them to prove the joker wrong? So why would they listen to him about "blowing the other ship being the ethical thing to do" when in the real world it isn't? On the last question, they do think it has bearing on their debate because Joker thought that at first, right before he decided to set the ferry thing up. Once the joker thought it would prove his theory it was up to the people and batman to prove him wrong and sabotage the complete execution of Joker's plan. That said, 'proving anything' is only a side-part of joker's activities (although that side-part builds up to his biggest trick and goal) and those activities are to just break order and cause chaos. He was gonna blow up both ferries even if they didn't blow each other up which means he either wouldn't accept he's wrong or he just believes he's right and wouldn't think that this test proves everything anyway (especially since he did still have Harvey up his sleeve).
3) If the people on the boats did not believe the Joker, or if they did but still didn't intend to blow up the other boat before the deadline, then why didn't they just jump off the boat?
Some were probably not alone and if you're with a family over there it takes one to not know how to swim then you're gonna have to stay there. Some just didn't know how to swim. Some probably feared that if someone jumps then that might set off the bombs. The desired feeling of the scene and what was going on was to be like what a person would be like if he was sitting on a mine. He can't move. He can't do anything. Most importantly the sceen just wouldn't work so some 'logical reactions' that we can imagine for people in a similar situation have to be discarded because you can't put everything in there and expect it to work with all the desired effects.
4) Even if the whole setup had made sense, and the choices of the people on the ferry could reflect badly on their morality, what would it prove if the boat of criminals had made the immoral choice? A group of criminals making an immoral choice hardly reveals something new about humanity.
The whole point of the ferry scene AND the prisoner's dilemma is that both elements (prisoners and citizens in ferry scene or both prisoners in prisoner's dilemma) are equals in this. In the result, as it was in the movie, the prisoners were presented as less cowardly in fact, probably even more moral within the dilemma. As social status though and human beings all of em were supposed to be equal so one failing would fail all, regardless of who it was. You have read the prisoner's dilemma thing right?
The situation with the two ferries is a classic example from game theory, also known as the prisoner's dilemma. In the prisoner's dilemma, two suspects are arrested by the police. The police visit each of them to offer the same deal. If one testifies (defects) for the prosecution against the other and the other remains silent, the betrayer goes free and the silent accomplice receives the full 10-year sentence. If both remain silent, both prisoners are sentenced to only six months in jail for a minor charge. If each betrays the other, each receives a five-year sentence. Each prisoner must choose to betray the other or to remain silent. Each one is assured that the other would not know about the betrayal before the end of the investigation. The unique equilibrium for this game is a Pareto-suboptimal solution-that is, rational choice leads the two players to both play defect even though each player's individual reward would be greater if they both played cooperatively. The same goes for the people on the two ferries. If one group decides to blow up the other, they go free (cooperation, so to speak, with the Joker) and vice versa. Otherwise, they'll run the risk of being blown up themselves. If neither group does anything, they'll both be blown up. The fact that neither group decides to blow up the other would be, according to game theory an irrational decision given the stated terms. The only reason it ends well is that the Joker doesn't succeed in detonating the device to blow up both ferries.
A lot of dilemmas or paradoxes call out for mathematical solution to the problem so I'm not sure what people have done to try and solve it but with the use of analogies and examples like this one one suggests that the solution is that in this case the best option would be no one to do anything because that's the only way one could lead to the optimal result.
Similarly in the ferry scene if the prisoners blew up the citizen boat it wouldn't matter that the PRISONERS did it, it would matter that someone did it AT ALL because that someone compromises the whole thing regardless if he's a prisoner or not. All one should know about this scene is that both ferries were full of citizens or that both of them were full of prisoners. One being with prisoners could serve only as a distraction to the solution of the dilemma and eventually the understanding of the scene.