A conspiracy to attack dozens of locations across multiple states? Without numerous leaks and large amounts of evidence? A conspiracy on that scale would involve hundreds or thousands of people - many of them sloppy and loose-lipped. Calling that conspiracy theory absurd would be an insult to absurdity!
My opinion, pending better and more complete information, is that Chipotle sacrificed their customers on food conspiracy-theorists' and Luddites' altar to ward off those groups' bogeymen, More plainly, by eschewing major producers and processors - so as to get organic, "locally sourced", non-GMO, etc. ingredients - Chipotle went with more marginal sources, and customers paid the price. A secondary possibility (i.e. in addition to, not instead of) is that Chipotle stores hired a lot of people recently in response to an anticipated volume increase due to holiday shoppers eating out instead of at home, and some stores' food handling training was poor (or not followed).
There's a reason "Big Food", "Big Ag", and the other bogeymen don't want to kill off people who use their products. Killing today's customers mean fewer and fewer customers in months, years, and decades to come.
