Preheat oven to 350°F.
Heat oil in a large skillet over medium-high heat Add the ham, apples, and onion. Cook until tender, about 5 minutes; set aside.

Cook pasta according to package directions; drain and set aside.

In a large saucepan melt 2 tablespoons of butter over medium heat. Stir in flour and ground black pepper until combined. Add milk and cream. Cook and stir until slightly thickened and bubbly. Add both mustards and both cheeses, stirring until melted. Stir pasta, along with the ham, apple, onion mixture. Transfer to a 2-quart square baking dish sprayed with non-stick cooking spray.
In a medium bowl mix melted butter and panko until crumbs are coated with butter. Sprinkle mixture over pasta in the baking dish.
Bake, uncovered, for 25 to 30 minutes. Sprinkle with fresh thyme, and serve.