Lightly spray a shallow baking dish with nonstick cooking spray (dish should be large enough so halibut fits in a single layer.) Preheat oven to 375 degrees F.
Heat the olive oil in a large pan over medium heat and add in the onion. Saute the onion until just golden, about 4 minutes.
Stir in the orange juice, orange zest, tomato, honey, and thyme and cook, stirring often, until thickened, about 3 to 5 more minutes. Remove from heat and cool for about 10 minutes.
Place 1/2 of the sauce mixture into the baking dish. Top with halibut fillets, sprinkle with salt and pepper, and cover with the remaining sauce. Cover with foil and bake until fillets are opaque, about 12 minutes.
Remove fillets to individual plates and keep warm.
Place juices from pan into a pot and boil over medium heat. Cook until sauce is reduced and thickened, about 2 minutes.