Heat the oven to 350 F. Cook quinoa according to package directions. Set aside.
Heat a large saute pan to medium-high heat. Add oil, zucchini, tomatoes, onion, celery, walnuts, garlic and thyme. Reduce heat to medium after 2 minutes. Once vegetables are tender, add cooked quinoa, salt, pepper and cheese.
Place the pepper halves on a baking sheet. Place 1/2 cup of the quinoa and vegetable mixture into each pepper half. Cover with foil and bake for 15 to 20 minutes. Uncover and bake for an additional 5 minutes until peppers are cooked to desired doneness.