We all know that it's a common trope in science fiction for ideas about divisions of race to be transplanted to racial boundaries – as if the authors are saying, “Look, if they can get along with wookies, why can't we humans all get along among ourselves?” It's such a common device, in fact, that it becomes difficult to recognize when alien species are actually not supposed to represent ethnicities. However, the Bugs from Starship Troopers may actually be something different – for lack of a better term, I'll describe their presence as a force of Nature, not Race (with a capital R) in the book.
Simply put, the relationship between the humans of the Terran Federation and the Bugs doesn't resemble racial conflict – the only interactions between the two are acts of destruction. Historically, racial conflict doesn't take the form of immediate, all-out war: the Europeans and American Indians were able to participate in trade and exchange of ideas before prejudice and hatred built up to cause the two sides to begin fighting each other; trade in slaves from Africa was facilitated at least by the cooperation of some leaders within that continent; even the American Civil War was not fought as a battle of “black versus white” at all. However, in Starship Troopers, the two sides are not just completely at odds with each other militarily: the Terran Federation “[understands] [the Bugs] as little as [it] [understands] termites” (222). The Terran Federation doesn't even have the faintest idea what the Bugs' motivation is for fighting or when it might be possible to declare peace – they don't even really know how bugs live, other than the very basics.
The relationship between the bugs and the humans appears most obviously in Johnny's proof about war as a cause of population pressure: “Either we spread and wipe out the Bugs, or they spread and wipe us out–because both races are tough and smart and want the same real estate” (186). This begins to resemble the conflict between American Indians and Europeans, but in the case of the American Indians, as members of the same species, they ended up becoming somewhat mixed in with the European population that invaded – no such thing is possible (as far as we can see) with the Bugs. The conflict is meant to be seen in a similar situation as that of the “retarded” wildlife of Sanctuary - “When types that had evolved on a planet enjoying high radiation and fierce competition were introduced, the native stuff was outclassed” (155). The humans and the Bugs in Starship Troopers don't communicate, they don't intermarry and they certainly don't hold Thanksgiving dinners together before killing each other: they're opposing species from different environments, and when they come into conflict, it's kill or be killed.
You raise some really good points here, of course. But I also wonder about the extent to which colonialist discourses from the 17th century forward used similar notions -- seeing the aboriginal inhabitants of a land about to be colonized as just another form of the local fauna -- in order to justify projects of racial subjugation and extermination. These are representations that are quite alien -- so to speak -- to our contemporary understandings of race, but they grounded many early modern racial projects...