Preheat oven to 400 degrees, slice spaghetti squash in half, lengthwise, and scoop seeds out with spoon. Place cut side up in baking dish with a small amount of water in bottom of dish, cover with foil or lid and bake 45 minutes to 1 hour, until squash just begins to shred fairly easily with a fork. Don't overcook or it will become mush!
While squash is cooking, brown sausage in a large oven-safe skillet. Once cooked, set aside on paper towel-lined plate. To your skillet, add onion and saute until translucent (about 5 minutes). Add garlic and cook for 30 seconds. Add tomatoes, spices and honey. Simmer for 30 minutes. Add sausage to sauce and simmer 10 more minutes.
Scoop out spaghetti squash with a fork, add to sauce and stir. Top with Parmesan cheese and bake 15 minutes.