Excellent idea! It makes me think of a fantasy book with cities close to your concept (it wasn't turtles but mythical beasts). in this book, the city and its inhabitants is a kind of a symbiot with the giant beast : they free it of its parasits and problems, took resources from its waste (like used scales for building, etc.).

Do you intend to consider the turtle as unique? I mean, other turtles with the same size would pose possibilites or problems for the city.