Preheat oven to 425 degrees. Lightly spray a baking sheet with non-stick spray.
Heat tablespoon oil in a skillet over medium heat. Add the onions. Cook until they soften, about 10 minutes. Add in chicken, cumin and pepperjack cheese. Cook until the cheese has melted and the chicken is warmed through. Transfer to a plate.
In the same skillet, heat just enough oil to coat the bottom of the skillet. Fry the tortillas, one at a time, until soft and pilable. About 30 seconds per side.
Place a heaping tablespoon of the chicken mixture in the center of each tortilla and roll up. Place the taquitos seam side down. Repeat with remaining ingredients until you've made 12 taquitos.
Cook taquitos preheated oven 15 minutes or until crisp.
While taquitos are cooking, combine green chilies, garlic, cilantro and jalapeno (if using) in a food processor and pulse a few times. Transfer to a small pan and cook over medium heat to heat through and cook the garlic a bit, about 3 minutes. Remove from the heat and allow to cool.
Remove taquitos from the oven and transfer to a serving platter. Just before serving, stir yogurt into the cooled green chile mixture, season to taste with salt and pepper and spoon over the top. Serve.