For the chicken: Arrange onion, celery and carrots in bottom of slow cooker. Season chicken thighs with salt and pepper and arrange over vegetables.
In a medium bowl, whisk together tomato sauce, lime juice, chipotle chiles with sauce, and garlic. Pour mixture over chicken.
Cover and cook on low for 6 to 8 hours or high for 3 to 4 hours. Serve half of the thighs with this meal (topped with diced avocado and cilantro and garnished with lime wedges) and reserve remaining thighs for another meal.
For the rice: In a medium saucepan, combine rice, coconut milk, water, beans, thyme, and lime zest. Set pan over high heat and bring to a simmer. Reduce heat to low, cover and simmer 5 minutes, until liquid is absorbed. Fold in scallions and season to taste with salt and pepper.