Heat oven to 400° F. Heat 1 tablespoon of the oil in a large saucepan over medium-high heat.
Add the onion, celery, and carrots. Cook, stirring occasionally, until the vegetables begin to soften, 3 to 4 minutes.
Add the tomatoes and their liquid, ½ cup water, salt, and pepper. Bring to a boil. Add the chard and simmer, stirring, just until wilted, 1 to 2 minutes.
Stir in the beans and 1 cup of the Parmesan. Transfer to an 8-by-11-inch baking dish or a shallow 2-quart casserole.
Cut the baguette in half crosswise, then lengthwise, into ¼-inch-thick slices. Brush one side of each slice with the remaining oil.
Arrange the slices, oiled-side up, over the vegetables, overlapping slightly. Sprinkle with thyme and the remaining Parmesan. Bake until bread is golden brown, 15 to 20 minutes.