Prepare pasta according to package directions. Drain and keep warm.
Sauté ham and onion in a large nonstick skillet coated with cooking spray over medium-high heat 5 minutes; stir in peas and next 3 ingredients. Set aside.
Melt butter in a large saucepan or Dutch oven over medium-low heat; whisk in flour until smooth. Cook, whisking constantly, 2 minutes. Gradually whisk in milk, and cook, whisking constantly, 5 minutes or until mixture is thickened. Remove from heat.
Stir in 1 1/2 cups cheese, stirring until melted. Stir in cooked pasta and ham mixture. Sprinkle with remaining 1/2 cup cheese. Serve immediately.