Rocksteady decided early on that the Joker would die in the story, and developed the idea of him poisoning Batman with the same affliction, in order to show how the two diametrically opposed characters would interact in pursuit of a shared goal. Warner Bros. and writer Paul Dini did not oppose killing off the character as long as it was not done for shock value, and as long as they made it clear that Batman was not at fault, since he would not intentionally kill someone.
Contributed by DrakeVagabond