Important:
This answer is based on tax law for the tax year ending 28 February 2020.
Answer:
The relevant requirement that disqualifies the person from being registered as a micro business, is not related to the number of employees employed by the business (individual). It is rather that the "qualifying turnover" of that person for the year of assessment does not exceed an amount of R1 million. See paragraph 2 of the Sixth Schedule to the Income Tax Act. That is relevant to the last year of assessment.
The other problem is that an application to register must be made before the beginning of the year of assessment. It can therefore not be made in respect of past years of assessment - see paragraph 8(1) of the Schedule.
The individual should consider making a voluntary disclosure.