The answer to your question is yes. The reality is that mass marking of hatchery-produced salmon actually helps with the genetic integrity. We can identify hatchery salmon. We can remove them from systems before they spawn. We can carefully select brood stock or progeny for hatcheries to ensure that we don't create domesticated fish by breeding hatchery salmon with hatchery salmon.
So the answer is that mass marking should actually be able to help with genetic integrity, not hurt.