Arrange fish in single layer in 13x9x2 glass baking dish. Mix lime juice, green onion, garlic, thyme and chile in small bowl; season with salt and pepper. Spoon over fish; let stand at room temperature at least 20 minutes and up to 1 hour.
Heat oil in large nonstick skillet over medium-high heat. Sprinkle fish on both sides with salt and pepper, then flour. Working in batches, add fish to skillet and cook until golden and opaque in center, about 2 minutes per side.
Cut off then slice from each warm pita forming opening. Stuff with fish, lettuce and tomato. Serve with desired condiments.