Preheat oven to 425°F. Brush a 9-by-13-inch baking dish with 1 Tbsp. olive oil. Scatter chopped onion and tomatoes all over bottom of baking dish and place fish on top, skin side down. Surround fillets with olives, sprinkle with thyme and drizzle with remaining 1 Tbsp. oil. Season fish with salt and pepper and cover loosely with foil. Bake until fish is flaky and firm, about 25 minutes.
Transfer fish to individual warmed plates. Spoon tomato-onion mixture and juices from baking dish evenly over fillets. Sprinkle with additional thyme, if desired. Serve warm.