Step 1Heat the oven to 375 degrees. Choose a baking dish just large enough to hold all of the tomatoes. Smear the bottom and sides with olive oil. Thinly slice one of the onions and scatter it across the bottom of the baking dish.
Step 2Mince the remaining onion and cook it slowly with 2 tablespoons of olive oil in a large skillet until fragrant, about 5 minutes. Add the garlic and the prosciutto and cook until the onion is softened, about 5 minutes.
Step 3While the onion is cooking, slice the top half-inch off of each tomato and reserve the tops to use as lids. Using a spoon or melon-baller, scoop out the pulp of each tomato, being very careful not to break the sides. Sprinkle the insides of the tomatoes lightly with salt.
Step 4Chop the pulp and add 1/2 to 3/4 cup of it to the onions. Cook until the pulp begins to melt, about 3 minutes. Add the rice and cook another minute. Stir in the pine nuts, 1 teaspoon of salt and the white wine and remove the pan from the heat. The mixture should be soupy; you should have about 2 cups of filling.
Step 5Pour the crushed tomatoes into the baking dish and stir it to lightly coat the bottom. Place the tomatoes cut side-up in the baking dish on top of the onions and crushed tomatoes. They should sit upright; if they don't, cut a thin slice from the bottom of each tomato so that they will.
Step 6Spoon the rice filling into the tomato shells, but don't overfill them--the rice will swell as it cooks and can easily burst the sides of the tomatoes (indeed, big beefsteak-type tomatoes have such thin walls that collapse is almost inevitable). Large beefsteak tomatoes will hold 3 to 5 tablespoons of filling each; smaller tomatoes will hold 2 to 2 1/2 tablespoons each. Drizzle a little olive oil over each tomato and replace the tops at a jaunty angle.
Step 7Cover the baking dish tightly with foil and bake 20 minutes. Remove the pan from the oven and spoon some of the liquid from the bottom of the pan over the rice. Replace the foil and continue baking, basting every 20 minutes or so. Cook until the rice is swollen and chewy but not chalky at the center, 40 to 60 minutes.
Step 8When the rice is cooked, remove the foil and the tomato lids and sprinkle the top of the rice with the grated cheese. Return to the oven and bake until the cheese has browned lightly, about 10 minutes.
Step 9Replace the lids and let stand 10 minutes before serving hot, or serve warm.