In a medium saucepan, bring the milk to a boil. Add the polenta and whisk until smooth. Cook over moderate heat, stirring, until thickened, about 5 minutes. Season with salt and pepper and stir in the onions, Fontina and 1 teaspoon of thyme. Spread the polenta in the crust and bake for 5 minutes, or until the top is lightly browned. Sprinkle with thyme and serve.