Heat 3 TBS olive oil in a large Dutch oven over medium-low heat. Add onion and garlic and saute until the onion is soft, but not brown. Mix in the chopped tomatoes, dried basil and red pepper flakes. Bring the mixture to a boil, breaking up tomatoes with the back of a spoon. Add the broth and once again, bring to a boil. Reduce heat to medium and simmer for 45 minutes, stirring occasionally. Stir in tomato paste and continue simmering for 30 minutes. Adjust seasoning.
Preheat oven to 375 degrees. Cook the pasta in a large pot of boiling water until al dente. Drain well and return the pasta to the pot. Toss with 2 TBS olive oil. Mix the pasta with the sauce to blend. Stir in the Havarti cheese and spread the mixture in a 13 x 9 x 2 inch glass baking dish. Sprinkle with olives (if desired) and top with grated Parmesan. Bake the pasta until heated through and bubbling (about 30 minutes). Top with chopped basil and serve immediately. 6 servings.