Preheat oven to 300°.
Heat a large nonstick skillet over medium-high heat. Coat pan with cooking spray. Add shallots; sauté 4 minutes or until golden. Add cumin and garlic; sauté for 1 minute. Add tomato puree and oil, and cook for 2 minutes or until thick, stirring constantly. Add honey and the next 5 ingredients (through chiles). Reduce heat; simmer for 10 minutes, stirring occasionally.
Combine beans and shallot mixture in a 2-quart baking dish. Bake at 300° for 1 hour or until thick and bubbly.