In my opinion the Vikings did wipe out the indigenous population. This is based on the lack of pre-norse names on the island.
The only other similar places where no indigenous place names survive are where such similar genocide took place. In more modern times, Tasmania being the oft quoted example.
Also, the Orkneys were the vital stop off point on all travels west for the Vikings and I cannot believe that they would have asked permission from the indigenous population to allow them to use the islands on a kind of 'lease back' scenario.
But there is a vociferous school of thought that argues the opposite, that the Orcadians and the Vikings coexisted in a mutually beneficial community.
I would guess that the distinctive Orkney accent should be attributed to the Norse influence more than any thing else.
FTC