It wasn't her money being lost. It wasn't coming out of her pocket. Her employees are paid hourly, they weren't losing anything either. She wasn't protecting anything but a couple bucks worth of company goods. She overstepped her bounds. That's not something a manager should do, even if she had good intentions. Company's don't want that. And as a manager representing Chipotle, she should know that. I've worked retail. In college I worked in the shoe department of a Sears, where people stole shit all the time. They'd just put their old shoes in the box and walk out with the new ones. And sometimes I'd get a person who I knew stole before come back. I wouldn't break company policy and ask them to leave a deposit or pay up front before trying shit on. That's ridiculous. That's not my place, and quite frankly, it's not my money. And I 100% would have been disciplined had I done that. It just creates too much potential for liability, and that's certainly not something you want out of your manager.
They hadn't done anything. If they steal, call the cops. Until then, follow company policy. Don't start treating people differently based on something you think they might do, or might have done a week ago.