Let me just say that I personally LOVE me some chipotle! It can definitely come in handy when you are in a pinch for food away from home or you want to suggest a place to eat among friends who may not be as into healthy eating as you are. That being said, you are RIGHT, everything they cook is soybean oil based...even if you got the carnitas, the peppers and onions are still sauteed in soybean oil.
To avoid the soybean oil you could do the romaine lettuce, carnitas, guacamole, and pico. Double the meat and maybe even the guacamole too.