Bring 6 quarts of water to boil in a large pot, and add 2 tablespoons of salt.
Meanwhile, in a 10- to 12-inch sauté pan, combine the olive oil, guanciale, onion, garlic, and red pepper flakes; set over low heat and cook until the onion is softened and the guanciale has rendered much of its fat, about 12 minutes.
Drain all but 1/4 cup of the fat out of the pan (and set aside to cook your eggs for tomorrow’s breakfast). Add the tomato sauce, turn up the heat, and bring to a boil, then lower heat to a simmer and allow to bubble for 6 to 7 minutes.
While the sauce simmers, cook the pennette in the boiling water for about a minute less than the package directions, until still very firm; drain.
Add the pasta to the simmering sauce and toss for about 1 minute to coat. Divide the pasta among four heated bowls and serve immediately, topped with freshly grated pecorino. Serves 4.