Whatever the potential abuses, I think fiction has a valid role to play in dealing with philosophical questions.
One example that comes to mind: I've observed in several discussions on the problem of evil that theists tend to want to discuss the matter in the most abstract possible terms. It seems to be easier to swallow a theodicy when you don't have the unpleasant facts of extreme suffering vividly in mind.
In the case of the POE, fiction can serve to cut through rationalizations in a way argumentation alone can never hope to do.
Eliezer, I hope you'll consider expanding this story into a novel. I'd buy it.