In a large, dry skillet, add the pine nuts over medium heat, and toast for about 5 minutes or until golden brown. Place in a small bowl and set aside.
In the same skillet, cook the ground sausage over medium high heat until browned, breaking up with a wooden spoon, about 5-7 minutes.
Reduce heat to medium, then add the minced garlic and shallot, and stir to combine. Cook until fragrant, 1-2 minutes.
Add the broth and shredded cheese, and stir to combine until mixed through and creamy.
Add in the cooked spaghetti squash and lemon juice, and stir to combine.
Remove pan from heat, then fold in the toasted pine nuts and basil pesto. Add salt and pepper to taste.
Stuff each pepper with the filling, and place the pepper tops on top.
Cover the baking dish with foil tightly, and bake for 40 minutes at 375 degrees F, or until peppers are tender.