Is an employee considered to have betrayed the company's trust and incurred sin if she performs the Dhuhr prayer with its Sunnah (ten rak'ahs), despite the employer's warning that only the Fard prayer is permitted?

Work must be disciplined by the Sharia (definition). It is not permissible to be late for work to perform supererogatory prayers if the manager does not allow it, because fulfilling the work contract is an obligation, and supererogatory prayers are recommended. The obligatory takes precedence over the supererogatory. One should try to explain the matter to the manager and request permission for a short time to perform the prayer along with its supererogatory parts, without prolonging them. If he does not agree, then the choice is between leaving the job or delaying the supererogatory prayers until returning home, if possible.