In a heavy bottomed pot, over medium low heat, melt the butter. Add the onion, jalapeño, and garlic, season with salt and pepper, and sauté until the onion is translucent, about 5 minutes.
Whisk in the flour, and once fully combined with the butter, whisk in the chicken stock, a little at a time, adding more once what you just added is fully combined. Adding it more quickly as you go, this should take less than a minute.
Add in the cumin, oregano, and green chilies and bring the stock to a boil. Add in the chicken, and turn the heat down to a simmer. You should still be able to see intermitent bubbles. Cook for 20 minutes or until the chicken registers 165 degrees on an instant read thermometer (the time this takes will vary depending on the thicknes off the chicken).
Remove the chicken from the pot, shred it, and return it to the soup. Stir in sour cream, milk, corn, and beans and cook until everything is warmed through, about two minutes. Serve topped with sliced avocado, sour cream, cheese, and cilantro.