First, a thief is not a "customer". Second, the employee is with his legal rights to apprehend said thief. Third, this policy will have the expected effect - many employees will remember this incident and will ignore acts of theft. Why bother doing anything about it when the store policy grants higher status to the thief than to the employee?
Especially since th eemployee made sure to make a citizen’s arrest. From that point on, he was technically outside store “police” and a part of our legal system in persuit of a criminal.