Cook pork: Put pork in a 3-quart heavy saucepan with salt, onion slice, garlic, thyme, and enough cold water to cover by 1/2 inch and bring to a boil, skimming foam. Reduce heat and simmer, partially covered, until pork is very tender, 1 to 1 1/2 hours. Cool pork in liquid, uncovered, 15 minutes. Drain, then cut pork into 1/3-inch dice. Discard onion, garlic, and thyme.
Make filling: Cook onion and garlic in oils in a 12-inch heavy skillet over moderately low heat, stirring, until softened, 5 to 8 minutes. Add tomatoes, thyme, bay leaves, cinnamon, allspice, cloves, nutmeg, 1 tablespoon vinegar, 1 1/2 teaspoons sugar, and 3/4 teaspoon salt and simmer, uncovered, stirring occasionally, until tomatoes have broken down and sauce is slightly thickened, 20 to 30 minutes.
While tomatoes simmer, cut an X in bottom of peach, then immerse in boiling water until skin begins to loosen, 10 to 30 seconds. Transfer peach to a bowl of cold water to stop cooking, then peel, pit, and dice (1/3 inch).
Discard bay leaves, thyme sprig, and cinnamon stick from tomato mixture, then add diced pork and remaining filling ingredients and simmer, uncovered, stirring occasionally, until fruit is softened but still intact, 8 to 10 minutes. Season with additional salt, sugar, and vinegar.
Make sauce: Purée walnuts and almonds in a blender with milk, cheese, 1 tablespoon sugar, and 1/4 teaspoon salt until smooth and silky, about 2 minutes. (Sauce should thickly coat back of a large spoon. If sauce is too thin, add more almonds and puré. If too thick, add more milk.) Season with salt and sugar.
Stuff and bake chiles: Put oven rack in middle position and preheat oven to 350°F.
Cut a lengthwise slit in each chile and carefully cut out seeds with kitchen shears, leaving stem intact. (For milder heat, carefully cut out ribs also.)
Divide pork filling among chiles, then close, overlapping sides of openings slightly. Transfer, seam sides up, to a 13- by 9-inch shallow baking dish, then cover with foil and bake until just heated through, 15 to 25 minutes.
Transfer chiles to plates, carefully turning them seam sides down. Pour about 1/3 cup walnut sauce over each chile, leaving some of chile visible, then sprinkle chiles with pomegranate seeds. Serve chiles warm or at room temperature.
Cooks' notes: Pork can be cooked 1 day ahead. Cool in broth, uncovered, then chill in broth, covered. Sauce can be made 1 day ahead and chilled, covered. Bring to room temperature before serving. Chiles can be roasted 1 day ahead. Chill, covered, then pat dry before filling.