Preheat oven to 400°F. Spread olive oil in bottom of a bake-and-serve dish just large enough to hold fish fillets snugly. Toss half of onion slices in oil and arrange fish on top. Cover with remaining onion slices and tomato.
Squeeze juice from lemon quarters over fish and place squeezed quarters around fish. Season with salt and pepper.
Bake, uncovered, until fish is translucent and flaky, about 15 minutes.
Put sour cream and horseradish in a small bowl; stir to combine. Season with salt and pepper to taste and stir well. Cover and chill until entire meal is ready to serve.
Spoon a small amount of sauce over fish while fish is warm and garnish dish with chives. Serve with remaining sauce.