Preheat the oven to 425 degrees F. Combine half of the red onion with the juice of 2 limes, the chopped chipotle, 1/2 teaspoon cumin and a pinch of salt in a bowl; set aside while you cook the pork.
Sprinkle the pork with the remaining 1 1/2 teaspoons cumin; season with salt. Heat a large skillet over medium-high heat. Add 1 tablespoon olive oil, then add the pork and brown on all sides, 8 minutes. Remove to a rimmed baking sheet; roast until a thermometer inserted into the center registers 145 degrees F, 12 to 15 minutes. Transfer to a cutting board.
Add the bell peppers and the remaining 1 tablespoon olive oil to the skillet. Cook over medium-high heat until slightly softened, 4 minutes. Add 1/2 cup water and 1/4 teaspoon salt. Cook until the water evaporates, 4 more minutes. Remove from the heat; add the onion mixture.
Toss the beans with the remaining red onion, the juice of the remaining lime, 2 teaspoons adobo sauce, the honey, cilantro and a pinch of salt. Slice the pork and serve with the beans and peppers.