Heat oven to 425°F. Rub the inside of a 2- to 2 ½-qt baking or gratin dish with garlic, then coat with oil.
Heat 1 Tbsp of the oil in a large skillet over medium-low heat. Add the onion and cook, stirring occasionally, until tender, 12 to 15 minutes (do not let it brown). Remove from heat and stir in the orange zest, orange juice and honey.
Scatter half the onion mixture in the bottom of the prepared dish. Arrange the tomatoes, overlapping slightly, over the onions and season with 1⁄4 tsp each salt and pepper. Repeat.
In a bowl, combine the bread crumbs, cheese, thyme and remaining Tbsp oil. Sprinkle over the tomatoes and bake until golden brown and bubbling, 15 to 20 minutes.