Cut a thin slice from the bottom of each squash half so they can stand upright. Place cavity-side-down in a 9x13-inch baking pan and cover tightly with foil.
Bake in the preheated oven until tender when pierced, 45 to 50 minutes. Remove from oven and leave oven on.
Break tempeh up into a bowl using your hands. Stir in sage, cloves, salt, and pepper. Transfer to a skillet over medium-high heat. Add apples, onion, raisins, cranberries, and thyme. Cook and stir until apples are tender when pierced, 8 to 10 minutes. Stir in pecans.
Turn squash halves upright. Fill equally with tempeh mixture and drizzle with maple syrup. Bake in the hot oven until filling is slightly browned on top, about 15 minutes more.