Is it permissible for an employee to pray alone or with some colleagues, in contravention of his minister's instructions which stipulate performing congregational prayer, thereby delaying the Dhuhr prayer beyond its prescribed time?

Prayer is permissible during any part of its time, and there is no harm in delaying the Dhuhr prayer as long as its time has not expired. If you fear the time will expire, then prayer becomes obligatory. Congregational prayer is an individual obligation, and obedience to rulers in matters that do not involve disobedience to Allah is an established principle. So, if the Imam delays the prayer within its prescribed time, it is better to wait for the Imam and pray with him, as was the practice of the righteous predecessors, to avoid discord and division.