One is the symbolism of April Fools Day that the story takes place on, a day when everything is reversed and topsy-turvy, including Two-Faces dual compulsions.
There are a few possible implications.That could explain why Harvey throws out the cards, he is already free.Morrison seems to be suggesting in the script that Two-Face is sparing the Batman as an act of compassion.Does this mean Harvey lied to save Batman or that he thinks that Batman punishment is to continue living in a mad world? At the final scene, we see him staring at the coin. Harvey reluctantly gets it and announces: He's free.
When Batman is surrounded by the inmates, he suggest to let Two-Face decide his destiny and gives him a coin.