Soak the beans in water to cover overnight. The next day, drain them. Peel the onion, and stud it with the cloves.
In a large saucepan, combine the beans, onion, bay leaf, sprig of thyme, and water. Bring the water to a boil over high heat, skim off the foam on the surface, and reduce the heat to medium-low. Cover and cook for about 45 minutes, until the beans are tender. Drain the beans in a colander and remove the onion, bay leaf, and thyme sprig. Let cool.
Preheat the oven to 400 degrees Fahrenheit.
Peel, trim, and mince the garlic. Wash and core the tomatoes. Grate them, one at a time, on the largest holes of a box grater.
In a skillet, heat the olive oil, add the garlic, and sauté, stirring, until it starts to brown. Add the sage and cook for 2 minutes. Add the grated tomatoes, stir to combine, and add the salt. Simmer, stirring once, for 15 minutes. Remove from the heat and let cool.
Spread the prosciutto out in a single layer on a baking sheet. Roast until crisp, about 10 minutes. Let cool.
In a large bowl, combine the beans and tomato-sage sauce. Crumble the prosciutto into the bowl, season with freshly cracked pepper, and serve.