Heat olive oil in a large nonstick skillet over medium-high heat. Add onion, and sauté 10 minutes. Stir in salt and anchovies; sauté 10 minutes. Stir in vinegar and chopped thyme. Reduce the heat to medium-low; cook 3 minutes or until liquid is absorbed, stirring frequently. Stir in olives. Cool to room temperature.
Preheat oven to 375°.
Trim crusts from bread; reserve crusts for another use. Lightly coat both sides of bread with cooking spray. Place 1 slice into each of 24 miniature muffin cups, pressing bread into pan to form cups (bread tips will stick up). Bake at 375° for 10 minutes or until dry and golden. Carefully remove the bread cups from pan; cool on a wire rack. Spoon 1 heaping tablespoon onion mixture into each bread cup. Sprinkle evenly with whole thyme leaves.