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Preheat oven to 450ºF with rack in middle.
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Cook bacon in a 12-inch heavy skillet over medium heat, stirring occasionally, until crisp. Transfer with a slotted spoon to paper towels to drain and add 3 tablespoons butter to bacon fat in skillet.
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Add onions and cook, stirring occasionally, until slightly caramelized, about 5 minutes. Add garlic, thyme sprigs, and salt and pepper to taste, then reduce heat to low and cook, stirring occasionally, until tender and golden, 10 to 15 minutes. Discard thyme sprigs.
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Put fish in a lightly oiled shallow baking dish and season generously with salt and pepper. Dot with remaining tablespoon butter and roast until just cooked through, about 8 minutes.
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Crumble bacon into onion mixture and stir in zest and thyme leaves. Serve each portion of fish topped with a couple tablespoons of onion compote and serve remainder on the side.
