Cook and stir smoked sausage and onion in a large saucepan over low heat until lightly browned, about 15 minutes. Stir in flour to coat sausage and onion. Gradually stir in milk, followed by half-and-half. Raise heat to medium and simmer soup until thick, about 5 minutes. Stir in thyme. Mix sauerkraut and its juice into soup and cook just until sauerkraut is heated through, 1 to 2 more minutes.