Place onion, parsley, cilantro, lemon zest, lemon juice, olives, capers, garlic and pepper in a food processor; pulse several times to chop. Add oil and process, scraping down the sides several times, until a pesto-like paste forms. Pat halibut with the herb paste. Cover and refrigerate for 30 minutes.
Preheat oven to 450°F. Coat a 7-by-11-inch baking dish with cooking spray. Arrange the halibut in the dish and spoon any extra herb mixture on top. Bake, uncovered, until the fish is opaque in the center, 15 to 20 minutes. Serve immediately.