Bacon is just one of many food items used for flavoring in foods. Removing it would, I assume, have a negative impact on the flavor of the food, otherwise Chipotle wouldn't have chosen to include it in the first place.
The "pork flavor" of Carnitas and the "pork flavor" in the beans aren't the same thing, and to suggest they are interchangeable (or that people order the pinto beans thinking that it is the only way to get "pork flavor") makes no sense to me. Most people, at least repeat customers, are getting the pinto beans because they have tasted them before, and decided they like the taste, not that they feel some need to increase the porkiness of their meal.
Every time I order a "vegetarian" bowl I am reminded that the pinto beans contain pork, so I assume this is an issue they have been aware of for a while. It makes sense to put a disclaimer and continue exactly as they have.
It makes little sense to alter their recipes to avoid every potential ingredient that might cause issue.