I don't know much of anything about this place called 'Chipotle', as I've never really seen such a place in my travels around the Commonwealth, nor in my Storm Chasing adventures; However, I am willing to bet that each individual restaurant will end up being like each individual Starbucks, or Subway, insofar as the larger company being against carry/firearms, while each individual 'store', whether by policy or personal actions, is left to decide to tolerate carry/firearms, or not.
I've been open carrying in every Subway in my home-town, in neighboring towns, in far-off towns, in long-distance towns, from Paducah, to Ashland, and Somerset, to Covington, and have yet to have any Subway employee, or manager, tell me to leave, or call the police on me, or anything negative. Every 'store' I visit, the staff are polite, and friendly, and if its a guy making my sandwich, will talk to me about his EDC pistol, or about how he always heard bad things about my carry pistol (Hi Point).
The same with Starbucks that I've openly carried in and out of whenever I did stop there, most of the time it's a police smile and a nod at the 2$ bills that I pay with every time I go to a Starbucks, and sometimes I'll have a assistant, or actual manager, say that they disagree with company policy, and welcome anyone who responsibly open carries.
I doubt if gun-friendly managers, assistant managers, or staff of each individual chipotle's will be keen on enforcing company policy.