Heat oven to 400°F. Cook the 1 cup orzo pasta according to package instructions, drain and transfer to a medium bowl. Add 3 tablespoons oil, the 4 ounces diced ham, 2 tablespoons chopped parsley, 2 sliced scallions, 1 clove minced garlic, and 1 teaspoon minced fresh thyme and season with salt and pepper to taste. Add 1 beaten egg and stir until coated.
Core the tomatoes, remove seeds and flesh with a spoon. Cut the peppers in half lengthwise and scoop out the seeds and core. Place vegetables cut side up in a medium 2-3 quart baking dish. They should fit snuggly so they don't fall over. Drizzle vegetables with oil and season generously inside and out with salt and pepper.
Divide mixture evenly between vegetables, mounding slightly on top. Fill baking dish with enough water to reach 1/2-inch up the sides of the tomatoes and bake, basting every 15 minutes, until vegetables are tender and orzo starts to brown, about 40 to 50 minutes.