Obviously this is a very poignant episode, and based on the scene where Fry's family comes to get the dog from the Cryogenics lab it's clear the dog is the only one who loves him. Bender jumping in the lava to get the dog showed he had come to terms with Fry's love of his dog and that everything would be all right. So, Fry's abrupt "decision" to stop the machine from cloning his companion was just the writer's way of getting to the ending they wanted. And what an ending. It was so devastating and tragic since Fry assumed his dog lived a happy life after he was gone but the truth was he suffered and grieved for over a decade. This level of tragedy I'd expect in a French film, not a Futurama episode. The dog waited for Fry, endured for Fry for so long. Fry was supposed to help his friend.
Science fiction punishes the rash and the evil by ensuring they face the consequences of whatever they did with the help of science. Similarly, science fiction should reward endurance and sacrifice and values such as friendship and companionship. I hope they "revisit" this storyline in the new episodes starting in 2008 because Fry owes it to his friend to make this right, just as the writers owe it to us.