Place beans in a large bowl, and add cool water to cover. Cover bowl, and let stand at room temperature for at least 4 hours or up to 8 hours.

Drain beans; discard soaking liquid. Place beans in a 5-quart pot. Add 8 cups water, chopped onion, 1 cup scallions, garlic, thyme, chile, black pepper, and cloves; bring to a boil over medium-high. Reduce heat to medium-low; simmer, uncovered, stirring occasionally, until beans are tender, 1 hour and 30 minutes to 2 hours, adding more water as needed. Discard thyme sprigs and chile.

Transfer about half of the beans and their cooking liquid to a blender. Secure lid on blender, and remove center piece to allow steam to escape. Place a clean towel over opening; process until smooth, 10 to 20 seconds. Stir pureed beans back into pot with remaining beans.

Heat 1/4 cup oil in a large skillet over medium. Add sliced onion, 1 tablespoon salt, and remaining scallions (about 1/2 cup). Cook, stirring occasionally, until fragrant and just beginning to brown, 4 to 6 minutes. Stir onion mixture into pot with beans, and bring to a simmer over medium-low; simmer, stirring occasionally, until flavors meld, about 15 minutes, adding additional water as needed to thin mixture to a thick, souplike consistency. Season with additional salt to taste. Cover and keep warm over low until ready to serve.

While beans simmer, combine rice, remaining 2 1/2 cups water, remaining 1 tablespoon oil, and remaining 1 teaspoon salt in a medium saucepan. Bring to a simmer over medium, and cook, uncovered and undisturbed, until water level is even with rice in pot, 2 to 4 minutes. Reduce heat to low; cover and cook, undisturbed, until water is completely absorbed and rice is tender and fluffy, 15 to 20 minutes.

Spoon rice evenly into 6 bowls, and top with beans.