Heat a soup pot over medium-high heat. Add 1 tablespoon extra-virgin olive oil and 1 tablespoon of butter. When butter has melted, add the onion and carrots and cook until vegetables are soft, about 5 minutes. Season with salt and pepper. Deglaze with the orange juice and simmer for 1 to 2 minutes, scraping the bottom of the pot with a wooden spoon.
Transfer the mixture to a food processor or a blender. Puree the mixture until smooth, then return to pot over medium heat. To mixture, add the frozen butternut squash puree and the chicken broth and stir to combine. Adjust the seasoning. Bring to a boil, then lower the heat and let simmer for 10 minutes. Grate some fresh nutmeg and stir to combine.
Ladle soup into bowls and garnish with chopped thyme and orange zest.