Simmer the shell beans in a large pot for 40 minutes with the water, thyme, half the garlic and freshly ground pepper. Check to see if the beans are tender, and if not, cook for up to but not beyond an additional 10 minutes. Add salt to taste.
Cook remaining garlic and sage in olive oil on low for 1 minute in a large skillet. Add sliced sausage, tomatoes and 1/2 cup of the bean liquid, which shouldn't be removed from the bean pot before at least 30 minutes of cooking. Simmer the sausage and tomato mix covered for 15 minutes.
Drain beans and reserve 1 cup of the liquid, removing thyme stems. Add beans to sausage and tomato mixture and simmer 10 minutes.
Cook pasta and drain. This can be done during the bean simmering stage. Add to bean mixture and add additional bean broth, if a souplike consistency is desired. Toss with olive oil, salt, pepper and vinegar and garnish with additional thyme sprigs.