Cut off 1/2 inch from the top of each tomato. Finely chop enough of the tops to equal 1 cup; set aside. Remove and discard the seeds and pulp from tomatoes.
In a large bowl stir together the chopped tomato, 3/4 cup of the bread crumbs, the beans, pine nuts, cheese, basil, 1 tablespoon olive oil, garlic, salt, and black pepper. Spoon the bean mixture into the tomatoes. Place the stuffed tomatoes in a 2-quart square baking dish.
In a small bowl stir together the remaining 3/4 cup bread crumbs, 2 teaspoons olive oil, and the thyme. Sprinkle over tomatoes.
Bake, uncovered, in a 350 degrees oven about 20 minutes or until crumbs are golden brown and tomatoes are heated through.