Funnily enough they did leave the indigenous to continue as they were, striking deals with the kingdoms to mine certain areas and providing lucrative (subjective to the tribesmen) "payments" in exchange for mining labour power which admittidly was a form of exploitation in economical terms, although was willingly accepted by them. They were not forced off their land or eliminated, but instead exposed to "exotic luxury". The tribesmen and women became aware of the prospects of working for the colonists in hopes of obtaining unimagined luxury, exotic commodities and a desire to be a part of an economy they did not understand. As the allure became more well known, members started to abandon tribal life to move to the colonists cities in hopes of obtaining more. All of this before "apartheid era" governance.

The result of the influx of indigenous people in the cities is what lead to apartheid, where a bunch of fools with superiority complexes tried desperately to preserve the home their settler ancestors created, by attempting to keep the indigenous under control through segregation and "law enforcement" by force.

Yes, they did need a permit to enter the cities, and they were required to populate only certain areas around the cities as a form of control. So I ask you, at what point did the government ban tribes from operating and why did indigenous people no longer have a desire to return to those kingdoms and lifestyles?

Are you saying that these small areas of settlers stripped "traditional ways of life" by FORCE, and it wasnt due to the natural individual ambition to leave a simple tribal life in pursuit of material luxury and technological marvel?

No doubt that the mere existence of these "aliens" interrupted "traditional ways of life" but what can be done to fix that? The settlers of those times didnt have the knowledge to understand the circumstances of their existence on the indiginous populayion, they had their own goals, being exploration and colonisation.