The ending certainly didn't wrap up the story in a neat little package, did it? Heinlein leaves a bunch of questions up in the air. What will Mike do in the afterlife? What became of Mike's new religion? Oh, and what is the Earth's ultimate fate? You know, just little things like that.
Okay, so plot-wise it does wrap everything up pretty nicely. The story of Stranger focuses on Mike's life, so it naturally ends with Mike's death. But the inclusion of that last chapter in the afterlife suggests that the story will continue for eons to come. It's even hinted that Mike was the reincarnation of the Archangel Michael, making this story just one chapter in a much larger work.
Whether or not you read the ending as a true ending or as a new beginning is up to you as the reader. You get to create your own ideas about what's next and what is to come. You also get to decide whether or not the ideas presented in this story work or need to be worked on some more. In a way, you get to write your own story about a Martian named Smith, just like Jubal. Frustrating, sure, but also kind of neat.