Bring large pot of salted water to boil. Add pasta to water and cook until al dente, according to package directions. Drain and set aside.
Preheat oven to 350°F and lightly butter 9x13-inch baking dish.
In Dutch oven or large, deep sauté pan, heat olive oil over medium high. Sauté onion, red bell pepper and green bell pepper 2 minutes; add drained tomatoes and continue to cook until onion and peppers are crisp tender and tomato cooking liquid has thickened and mostly evaporated, about 5 minutes. With slotted spoon, remove vegetables from pan and set aside. Carefully wipe pan with paper towel.
In same pan, melt butter over medium heat. Sprinkle in garlic and flour and cook, whisking often, until flour is golden brown, about 2 minutes. Gradually pour in milk, whisking constantly, then half and half. Cook until sauce simmers and thickens, about 7 minutes. Remove from heat and stir in red pepper flakes, salt and oregano. Stir in Greek yogurt, mozzarella and fontina. Add drained pasta and sautéed vegetables. Stir to coat.
Roughly chop 2/3 of pepperoni. Stir into pasta mixture, reserving remaining pepperoni. Spoon pasta into prepared baking dish, then scatter olives and remaining pepperoni over top. Sprinkle with parmesan cheese and bake until hot and bubbly, about 20 minutes. Let rest a few minutes before serving.