Who is responsible for an employee wrecking a customer's vehicle because of running a stop sign?

It deepends on company policy. Most likely, the company has insurance which will protect their interests, but that does not necessarily let the employee off the hook, unless company policy is to cover it for the employee. Otherwise, you may find your employer or the insurance company asking you to reimburse them. But in a situation where employees drive customers' cars, I can't imagine there isn't a written policy covering just this eventuality. And I can't imagine you haven't read and signed a copy of it.