In a medium pot, bring a few inches of water to a boil over medium heat, then salt the water. Trim the broccoli rabe and cut it into 1 1/2 to 2-inch lengths. Simmer in boiling water to reduce the bitterness, about 4 to 5 minutes, then cold shock in ice water and drain very well.
Heat a Dutch oven or large soup pot over medium-high heat with extra-virgin olive oil, a turn of the pan. Add the sausage and brown and crumble, 7 to 8 minutes. Add the onions, garlic and chile and cook a few minutes more. Add the thyme and lemon zest, then add broccoli rabe and season with a little nutmeg. Stir in the stock and the water and bring to a boil. Simmer a few minutes to combine the flavors. Turn off the heat, cool and store for a make-ahead meal. Reheat the stoup over low heat and bring to a low boil. Add the pasta and cook to al dente, about 10 minutes. Ladle the stoup in shallow bowls and garnish with cheese. Serve with crusty bread for mopping.