I recently went to Chipotle for I think the first time since the changes[1], and while I'm sure the food is safer, having the chicken cooked offsite ruins the texture. I'm not sure I'll go back any time soon.
[1] I didn't stop going because of the incident, I stopped going because I stopped doing what I was typically following with lunch at Chipotle.
I'm not suggesting that they weren't damaged by those incidents. 2016 data isn't in yet, but 2015 sales figures show them to be at least holding steady.
My point was that the company ultimately aggressively addressed the problem head-on and very well may have saved the company. The public has no long term memory. Let's compare notes in 2018.