Prepare the bacon according to package directions until crispy. Place cooked bacon on a few paper towels to dry and cool. Reserve one tablespoon of the bacon grease and discard the rest. Chop the bacon into small pieces, separating two slices worth of chopped bacon from the rest (reserved for garnish).
Place the tablespoon of bacon grease in a Dutch oven or soup pot and bring over medium heat. Add the onions and apples and stir to coat. Cook for 8-10 minutes until onions are translucent. Add the broth, salt, pepper, thyme and cinnamon and stir together. Bring the mixture to a boil and boil for 5 minutes until apples are softened.
Add the pumpkin, brown sugar and bacon pieces (4 slices worth) and stir until well combined. Reduce the heat to med-low and cook for about 10 minutes.
When soup is done cooking, add the cream cheese and puree the soup completely, either by using an immersion blender directly in the pot or by pouring the soup in batches into a normal blender, until smooth. Soup will be thick and creamy. Serve with the remaining bacon pieces sprinkled over top as garnish.