Combine first 7 ingredients in a Dutch oven; bring to a boil. Reduce heat; simmer 20 minutes. Add halibut; simmer 10 minutes. Remove from heat; let stand 20 minutes.
Heat oil in a large saucepan over medium heat. Add 4 1/2 cups onion and bell pepper, and sauté 5 minutes or until tender. Stir in flour. Add tomatoes and oregano; cover, reduce heat, and simmer 15 minutes.
Remove fish from cooking liquid with a slotted spoon; drain well. Discard cooking liquid and solids. Sprinkle fish with salt and black pepper. Arrange over rice. Top with tomato sauce. Serve with lemon wedges.