first off mcdonalds does NOT own chipotle at all. they are a public company and even though mcdonalds originally owned some of them, they divested years ago
chipotle ingredients are very good vs. other fast food places.. they strive to have grassfed beef, hormone free chicken, fresh guacamole, etc. however the portion sizes are simply too much to be considered 'healthy' for anyone who isn't underweight
a typical burrito for example is 1000 calories. that is a lot. if you want to eat there i would suggest not getting the tortilla or shell. just eat the other ingredients and keep your portions small... so get like a salad with toppings. maybe cut in half and take rest home for the next day