Sort and wash beans; place beans in a large Dutch oven. Cover with water to a depth of 2 inches above beans. Bring to a boil; cover, remove from heat, and let stand for 1 hour.
Drain beans, and return to Dutch oven. Add 6 cups water; bring to a boil. Cover; reduce heat, and simmer 30 minutes. Set aside.
Coat a large skillet with cooking spray; place over medium heat until hot. Add onion and next 3 ingredients; cook, stirring constantly, 7 to 9 minutes or until tender. Add basil and next 4 ingredients; cook, stirring constantly, 1 to 2 minutes.
Add onion mixture, remaining 2 cups water, broth, and next 4 ingredients to bean mixture; bring to a boil. Cover; reduce heat, and simmer 1 hour.
Pour 2 cups bean mixture into container of an electric blender; cover and process until smooth. Return mixture to Dutch oven; bring to a boil. Reduce heat; simmer, uncovered, 2 hours or until thickened, stirring occasionally. Remove and discard bay leaves. Stir in pepper.
Combine rice, cilantro, and salt; stir well. Spoon 1 cup rice mixture into each of 9 individual serving bowls; top each with 1 cup bean mixture. Sprinkle evenly with tomato.