Preheat oven to 400 degrees. In a large skillet, heat oil over medium-high heat. Add onion, garlic, 1/2 teaspoon salt, and 1/8 teaspoon pepper. Cook until onion is translucent, about 3 minutes.
Add sausage, and cook, breaking up with the back of a spoon, until lightly browned, about 4 minutes. Add tomatoes and 1 cup water; cook until slightly thickened, about 5 minutes. Remove from heat and stir in couscous.
Fill pepper halves with couscous mixture. Arrange peppers in a baking dish just large enough to hold them. Add 1/2 cup water. Cover with aluminum foil, and bake until peppers are tender, 35 to 40 minutes. Remove foil, and sprinkle with cheese. Return to oven and bake, uncovered, until cheese has melted and peppers are very tender, 10 to 15 minutes more.