Preheat the oven to 400 degrees F. Heat the oil in a medium saucepan over medium heat. Cook the garlic and onions until softened, about 5 minutes. Add the mustard seeds, paprika, salt, pepper and sage and stir until the spices become fragrant, about 20 seconds.
Add the beer, and when the beer foam subsides, increase the heat to medium high. Stir in the vinegar, molasses, pepper jelly (if using), tomato paste and navy beans. When the sauce comes to a simmer, turn the heat to medium-low and keep at a very low simmer until slightly thickened, about 15 minutes.
Transfer to a 1 1/2-quart baking dish. Bake until the sauce thickens to coat the beans, yet is still very saucy, and the beans have absorbed some sauce, about 40 minutes.