Preheat oven to 400 degrees. Melt butter in a medium skillet. Add onion; cook 2-4 minutes. Add salt, pepper, honey, Worcestershire, and thyme. Stir well. Cook another 2-3 minutes.
Add broth, and cook until onions are golden brown (about 12 minutes, stirring occasionally to prevent burning. When onions are golden, stir in zoodles.
Spray small baking dish with cooking spray. Pour zoodle mixture into dish. Top with gruyere cheese. Bake 20-25 minutes or until cheese is melted and golden. Remove from oven and let stand 5-10 minutes before serving. Garnish with fresh thyme, if desired. (If there is excess liquid from the zoodles, scoop it off with a spoon.)