Preheat oven to 350°.
Cut chiles in half lengthwise; remove stems and seeds. Set aside. Combine water and quinoa in a medium saucepan; bring to a boil. Cover, reduce heat, and simmer 13 minutes or until liquid is absorbed. Set aside.
Spray a large nonstick skillet with cooking spray; place over medium-high heat until hot. Add bell peppers, onion, jalapeño pepper, and garlic; sauté 2 minutes. Add pumpkin seed kernels; saute 2 minutes. Remove from heat; stir in quinoa, green onions, cilantro, soy sauce, and lime juice. Spoon 1/3 cup quinoa mixture into each chile half.
Pour tomato juice into a 13 x 9-inch baking dish; place stuffed chiles in dish. Cover and bake at 350° for 20 minutes. Sprinkle cheese over chiles; bake, uncovered, an additional 10 minutes or until cheese melts and chiles are thoroughly heated. Spoon tomato juice over chiles.