Heat the oil in a large pot over medium heat and add the onion and green pepper. Fry, stirring occasionally, until very soft - about 5 minutes.
Add the garlic and fry until tender - about a minute. Add the chopped tomatoes and fry, stirring occasionally, until beginning to break down into a thick sauce - about 10 minutes.
Add the cumin and oregano and fry for about a minute, stirring frequently, to bring out the flavour.
Add the pinto beans and vegetable stock. Raise the heat to bring to a boil and then reduce the heat to simmer for about 10 minutes to meld the flavours.
Place the chipotle pepper in a food processor or blender add 3 ladles of the bean soup. Blend until you have a thick puree. You can also ladle the soup into a smaller pot and use an immersion blender to make the puree.
Stir this puree back into the soup along with the salt. If you want the soup thicker, you can blend a few more ladlefuls until you reach your desired consistency.