Preheat the oven to 450 degrees F. Heat 1 tablespoon olive oil in a large skillet over medium-high heat. Add the jalapeno, garlic, thyme and half of the onion. Cook, stirring, until soft, about 3 minutes. Add the chicken, 1 teaspoon salt and 3/4 cup water. Bring to a boil, then cover and cook until the chicken is tender, about 6 minutes.
Remove the chicken to a plate. Transfer the cooking liquid and vegetables to a blender; add the tomatoes and allspice and puree with the lid ajar. Wipe out the skillet, add the remaining 1 tablespoon olive oil and place over medium-high heat. Add the tomato mixture and cook until slightly reduced, 6 minutes. Pour into a baking dish.
Brush the tortillas with olive oil and put on a baking sheet; bake 5 minutes. Shred the chicken. Top each tortilla with chicken and cheese, then roll up and arrange in the baking dish, seam-side down, spooning some sauce on top. Bake until the cheese melts, 4 minutes.
Toss the herbs, remaining onion, and salt to taste. Sprinkle on top.
Per serving: Calories 452; Fat 23 g (Saturated 9 g); Cholesterol 74 mg; Sodium 852 mg; Carbohydrate 35 g; Fiber 4 g; Protein 27 g