First of all, it's isn't exactly a straight line from killing orcs to killing indigenous people. The line goes:
Killing orcs <---- because they're stupid, primitive, promiscuous, savage == history of 'stupid, primitive, promiscuous, savage' being used to explain why some people are less human than we are ----> killing those people
Does that make sense? It's not the parallel of the killing, it's the parallel of the justification language.
Also it doesn't really matter AT ALL if some people don't think there's a connection between those two things, especially if those people are not members of the groups we are discussing. At least some members of those groups, and potentially a high percentage of them, do think there's a hurtful connection (not just in D&D or RPGs in general, but in any fiction).
And, even though I'm not in any of those groups, based on everything I've learned about psychology and trauma, I very much believe there's a relevant connection, and "being offended" or "being uncomfortable" doesn't do justice to the impact.