If God is real, then the supernatural is real and miracles are possible. That would include the miracles in the story of Jonah. If God is not real, then there is no supernatural (unless some form of pantheism is true). In that case, miracles like those described in Jonah are not possible and (in that case) your interpretation of Jonah as being in the context of mythological literature written to convey moral lessons is compelling. However, I believe God is very much real. All the best.