Cook bacon in a large nonstick skillet over medium heat until crisp. Remove bacon from skillet, reserving 1 teaspoon bacon fat in skillet; crumble bacon, and set aside. Add onion to bacon fat in skillet; cook, stirring constantly, 5 minutes. Add thyme and next 3 ingredients; cook, stirring constantly, 5 minutes. Sprinkle with flour; cook 1 minute, stirring constantly. Gradually stir in milk; bring to a simmer. Cook 5 minutes or until thick, stirring frequently. Remove from heat; stir in sour cream and chives.
Spread 1/2 cup sauce in an 8-inch square baking dish coated with cooking spray. Arrange one-third of potatoes over sauce, overlapping slices slightly. Spread 1/2 cup sauce over potatoes. Repeat layers twice with remaining potatoes and sauce, ending with sauce. Sprinkle with crumbled bacon. Cover and bake at 350° for 1 hour and 10 minutes or until potatoes are tender. Uncover and bake an additional 10 minutes. Garnish with thyme sprigs, if desired.