Heat the oven to 170 C / 340 F with a rack in the lower middle. Pat the beef dry with paper towels, then toss it with 1 tsp of the salt and the pepper.
Heat 2 tbsp of the oil in a 28 cm / 11-inch oven-safe Dutch oven over medium-high heat. Sear the beef in 2 batches, 5 to 6 minutes per batch, turning with tongs until the cubes are browned on at least 3 sides. Move each batch to a plate.
Lower the heat to medium and add the remaining 1 tbsp oil and the onion. Cook for 5 minutes, until soft. Stir in the garlic and tomato paste and cook for 1 minute, until the paste darkens. Pour in the wine, scrape up the browned bits from the bottom, and simmer for 2 minutes.
Return the beef and any juices to the pot. Add the crushed tomatoes, water, cinnamon stick, allspice, bay leaves and the remaining 1/2 tsp salt. Bring to a simmer, about 2 minutes, then cover and bake for 105 minutes, until a beef cube pulls apart easily with a fork.
About 10 minutes before the braise ends, heat the stock in a 1.5-quart / 1.4 L saucepan until steaming. Take the pot out of the oven, remove the cinnamon stick and bay leaves, and check the beef. If it still resists a fork, cover and bake 15 more minutes. Then stir in the orzo and hot stock, scraping the bottom, and bake uncovered for 25 minutes, stirring once at the halfway point, until the orzo is tender and most of the liquid is absorbed.
Let the pot stand uncovered for 10 minutes so the sauce thickens. Taste and add salt if needed. Sprinkle with the grated kefalotyri or Parmesan and the parsley and serve from the pot.