Preheat oven to 400 degrees.
Rub the inside and outside of each squash half with salt and pepper and ghee.
On a large baking sheet, place the squash halves, cut side up, and place in the oven. Bake for 15 minutes, until fork tender.
In a large skillet over medium heat, add the sausage and cook for 5 minutes, until brown. To the sausage, add the remaining ingredients (shallot through thyme) and sea salt and freshly ground black pepper to taste and stir. Cook for 10 minutes, until sausage is cooked through and vegetables are tender.
Spoon sausage mixture into the cooked squash halves and serve.