Heat the remaining 3 tablespoons of olive oil in a large skillet. Add the pancetta and cook over moderate heat until lightly browned, about 5 minutes. Add the shallots, sage, crushed red pepper and a generous pinch of black pepper and cook until the shallots are soft, about 4 minutes. Add the squash, rigatoni and the reserved cooking water and cook over moderate heat, tossing gently, until the sauce is thickened and the pasta is al dente, 2 to 3 minutes; season with salt. Stir in the 1/2 cup of Pecorino. Serve the pasta in deep bowls, passing extra Pecorino at the table.