As commissioned public officers, Notaries have a responsibility to obey state laws. They cannot ignore or break these laws, even if ordered to do so by an employer or other individual. That's why Guiding Principle V of The Notary Public Code of Professional Responsibility states:
V
THE NOTARY SHALL GIVE PRECEDENCE TO THE RULES OF LAW OVER THE DICTATES OR EXPECTATIONS OF ANY PERSON OR ENTITY.
Even if an employer paid for a Notary's commission, this does not give any employer authority to ask a Notary to waive essential elements of notarization such as the signer's personal appearance or identifying the signer. Also, an employer cannot force a Notary to resign a commission if the Notary changes employment. The commission belongs to the Notary and is the Notary's responsibility.