Heat a nonstick skillet coated with cooking spray over medium-high heat.
Add onion and next 4 ingredients (onion through pepper); saute 8 minutes or until lightly browned, stirring frequently. Stir in vinegar, basil, and oregano; cook 2 minutes.
Remove from heat.
Arrange beans in an 11 x 7-inch baking dish coated with cooking spray. Top with onion mixture. Arrange tomatoes on top of onion mixture, and sprinkle with cheese.
Bake at 400 for 35 minutes or until the cheese is lightly browned.