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Bring a large pot of salted water to boil. Add the pasta to the water and cook until al dente, according to package directions. Drain and set aside. Preheat the oven to 350 degrees F, and lightly grease a 9x13 or similar baking dish.
Melt the butter in a Dutch oven or similar large, deep pot over medium heat. Add the onion and sauté until beginning to soften, about 6 minutes. Sprinkle in the flour and garlic, then cook whisking often, until the flour is golden brown, about 2 minutes. Gradually pour in milk, whisking constantly, then the half and half. Continue to cook until the sauce simmers and thickens, about 7 minutes. Remove from heat, then stir in the salt and nutmeg, then the Greek yogurt, cheddar, and 1/2 the total amount of sage. Add the drained pasta, apples and ham, toss gently to coat, then transfer to the prepared baking dish.
Combine the bread crumbs and olive oil in a small bowl and sprinkle over the top of the pasta. Cover the dish with foil, then bake for 10 minutes covered, then uncover and bake 10 additional minutes, until the crumbs are golden and the pasta is hot and bubbly. If necessary, turn your broiler to high to finishing browning the crumbs, watching them carefully so that they do not burn. Remove baked pasta from the oven, sprinkle with remaining sage, and serve.