Heat 3 tablespoons oil in a Dutch oven over medium-high heat. Sauté onion and garlic for 5 minutes. Add tomatoes, basil and red pepper flakes; bring to a boil. Mash tomatoes with the back of a spoon, and then add broth. Reduce heat and simmer one hour. Add salt and pepper; set aside. Cook pasta according to package directions; drain. Toss with remaining 3 tablespoons oil and combine with tomato sauce. Stir in Havarti cheese. Pour in an ungreased 13 x9 casserole dish. Top with olives, and then Parmesan cheese. Bake, uncovered, at 375 degrees for 30 minutes. Sprinkle fresh basil on top before serving.