An employer doesn't have the authority to authorize its employees to violate the law. An employee who personally participates in a crime has both criminal and civil liability for the employee's actions.
Private sector employers have vicarious respondeat superior civil liability for the actions of their employees taken in the scope of their duties. In other words, anything that an employee of a private sector employer is liable for, the employer is also liable for.
Governmental employers do not have vicarious respondeat superior civil liability for the civil rights violations of the employees.
Direct civil as opposed to vicarious civil liability, and criminal liability for an employer (governmental or private) is generally limited to acts carried out by employees of the entity at the direction of senior management or pursuant to a policy, explicit or implicit, of the employer.
This said, it is the nature of large employers to break tasks into component parts spread over many employees in different parts of the employing entity. In some circumstances, an individual employee's role may be such that the employee lacks sufficient information about the overall course of action of the employer to know that their actions are part of an overall course of conduct by the employer that constitutes a crime or tort.
For example, to retreat to an old school example, suppose that there is an employee who sits in front of a shredding machine all day and feeds paper into and clears paper jams, etc. whose job is to shred whatever documents are put in a bin next to his work station. This guy, who makes no decisions regarding what is to be shredded and has no real knowledge of why documents are being shredded, probably doesn't have criminal or civil liability if his labor is used to illegal destroy some documents. For all the shredder guy knows, he could simply be destroying redundant copies of documents to free up space in the filing cabinets while a single archival copy is retained.
Typically, criminal laws require some level of mens rea (i.e. intent) which may be intent to do something in particular, it may be knowledge of certain facts, or what have you. An employee is generally only going to face criminal liability is the employee who carries out the wrongful act on behalf of the employer does so with the requisite knowledge and intent set forth in the criminal statute.