One of the things that Chipotle used to (and still, to some extent) do differently was that they turned raw meat into cooked meat onsite, rather than taking precooked frozen meat from central facilities and reheating it.
(They also purportedly have very stringent guidelines about what they permit to be done to the animals the meat comes from; I don't know what those requirements are, so I can't say how strict they are.)
The tradeoff with that, combined with their local sourcing guidelines, is that they'd have far more distinct pipelines and places that they needed to ensure a lack of contamination in.
The article covers them having now switched to an approach which opponents refer to as "precooking" the meat in large central facilities, to kill pathogens effectively, while also maintaining as much of their "fresh food prepared right in the restaurant" ethos as they can muster.
(Not being a chef, it seems like they basically cook the meat to something like medium-rare, slowly, but at sufficient temperature to kill pathogens, and then cool it and cook it the rest of the way at restaurants.)
I would imagine this sort of issue is one where it's easy to miss the forest for the trees. I was never really a fan of Chipotle to begin with, but wasn't bugged when I heard about the outbreak; it just seemed like a tradeoff in my mind for less processed meats - you naturally expose yourself to dangers like this. I wasn't aware that the fans of Chipotle thought differently, but apparently they did and I guess the chain mishandled the PR on the event?