Preheat oven to 375°F. Butter 9×13-inch baking dish and set aside.
Cook pasta according to package directions until al dente; drain and set aside. Meanwhile, cook bacon until crisp then chop into small pieces. Drain all but 2 tablespoons bacon drippings from pan then return to medium-low heat and add chopped leeks. Cook, stirring occasionally, until leeks are softened and just starting to brown, about 10 minutes. Stir in thyme and bacon; remove pan from heat and set aside.
In large heavy saucepan, melt butter over medium heat and stir in flour. Cook, stirring, about 2 minutes, until flour mixture has darkened slightly, then whisk in half and half. Bring sauce to boil, whisking constantly, then turn heat down and let simmer, stirring, until thickened.
Stir in 1 cup cheddar and 1 1/2 cups havarti cheese. Add salt and pepper then remove sauce from heat. Stir in pasta and bacon-leek mixture. Pour pasta into prepared baking dish and sprinkle with reserved cheddar. Bake 25 minutes.