Coat an oven-safe pot with olive oil and put over medium-high heat. Add the onions, peppers and crushed red pepper flakes. Season with salt, to taste, and cook until the onions and peppers are soft and aromatic, about 8 to 10 minutes. Add the garlic and cook for another 2 to 3 minutes.
Preheat the oven to 375 degrees F.
Add the sausage and use a spoon to help break it apart. When the sausage is brown, add the tomato paste and cumin and cook for 4 to 5 minutes. Stir in the Dijon, apple cider vinegar, and molasses, then add in the beans and 1 1/2 cups of water. Taste and season with salt, if needed. Bring to boil, then reduce the heat and simmer the beans until they are nice and thick and taste really good, about 15 to 20 minutes. After 20 minutes, add the remaining cup of water.
Top the beans with the bacon slices. Bake until the beans are nice and thick and the bacon is crispy, about 25 to 30 minutes. Remove from the oven and serve.