In a large saucepan, cook the crumbled Italian sausage with Italian seasoning, fresh thyme leaves, and red pepper flakes on medium heat. Stir regularly to break up the sausage.
Once the sausage has released its juices and is half cooked, add the uncooked orzo and minced garlic. Continue cooking, stirring constantly, for about 2 minutes on medium heat to lightly brown the orzo.
Pour in the chicken stock and add the cubed butternut squash. Stir well, cover with a lid, bring to a boil, then reduce to a simmer. Cook for about 5 to 10 minutes until the orzo and squash are tender.
Add the spinach to the soup, cover, and allow it to wilt on low heat, stirring occasionally.
Once the spinach has wilted, remove the soup from the heat, and stir in the heavy cream. Season with salt and pepper to taste. If the soup is too thick, add additional chicken stock or water. For more heat, sprinkle additional red pepper flakes.
Serve hot, topped with grated Parmesan cheese and additional fresh thyme.