Why think about it as necessarily being a metaphor? Why not an exercise in social/historical speculation? The augs aren't a class thing, since you have two groups of augmented: People who were rich and wanted to get a step ahead, and on the other hand industrial workers (even sex workers, that's a plot point in HR) who were not outright forced but strongly encouraged to get them (and presumably paid by their employers, not like they could afford to do it themselves). Also not directly a race thing, most augs, seemed to me, were white Czech people.
So of course the writers use language and things out of real life, because how else can you creatively create anything? But I think you are being to sensitive about this, but of course it's a view that is perfectly understandable. But my take is this: It's about how society deals with new forms of Others, in a world where individual rights are far beneath corporate ones, and furthermore you have things like the Illuminati controlling everything and everyone. (That was the cause of the Incident, after all, the chip controlling people)
This isn't a great setting to get real life lessons from (a bit muddled by the fantastic stuff), but I would see it as an appeal that 1) individual rights should come first visa-vi corporate ones (that's kinda social democratic) and 2) ``protecting'' people by segregation, no matter the justifications, will lead to terrible human suffering. (the Holocaust is not comparable here, think about the Gaza strip)
