I don't think it's all that mysterious. I think they are being sabatoged by Big Food because they are a threat to the current model of cheap mass produced chemical agriculture and feed lot meat.
They are the most high profile chain with a national presence taking advantage of the move toward cleaner food choices some of us are making. I don't want to eat GMOs and they get that and provide me an option to avoid those poisons. In the eyes of Monsanto, Chipotle must be punished.