The threat of the Covenant is not that of "racial mixing", nor is their threat one of diversity. The threat of the Covenant is their blind loyalty to a false religion propagated by the Prophet Hierarchs to hide the fact that Humanity is the legacy and part of the lineage of the Forerunners, the ancient race who saved the galaxy from the horiffic plague of The Flood. The Covenant itself has not only been largely enslaved and indoctrinated into believing a false religion by the High Prophets, it is being used to wage a Holy War against anyone in their path as they search the galaxy for the artifacts of the Forerunners, with a focus on the Galactically Genocidal Halo Rings originally built to eradicate the Flood, the infectious intergalactic parasite whose only motive is to devour all life in the universe.
Humanity is not waging a war on the Covenant the way a race purist would on those different from them, they are protecting themselves from the invasion of The Covenant on their genocidal campaign. They are largely unaware of the existence of the Forerunners until the final years of the Human-Covenant War, not knowing the true intentions of the Covenant until 2552, nearly thirty years after first contact on Harvest.
The SPARTAN program, originally commisioned by Dr. Catherine Halsey in early 2500 to prepare for a rebel uprising between Earth's colonies, was rife with doubts. Halsey was constantly questioning her methods and the way she treated her soldiers. The SPARTANS were meant to be the final line of defense and true soldiers in every sense of the word, having been taught battle from an early age. Halsey herself expressed that what she had done to the children was terrible and part of her hated herself for doing it, but she kept to her task. The SPARTANS were an idea that progressed into a full blown experiment which proved instrumental in the victory of humanity in the Human-Covenant War. Their motives were questionable and their origins were shady, but the SPARTANS proved to be an indespensible asset to the UNSC and Earth's colonies. If anything, the SPARTAN program is meant to show both sides of the military industrial complex, originally thought up by politicians fearing an uprising but then controlled and run by scientists who tried their best to keep their soldiers human while still training them to the best of their abilities. The genetic augmentation of SPARTAN soldiers was one of the riskiest parts of the program and in fact resulted in the deaths or deformation of more than a few of the SPARTAN recruits. Halsey doesn't ratiionalize what she's doing and in fact carries the burden of the pain of the SPARTAN program for all her days, but she realizes what the soldiers will mean for humanity, especially after First Contact with the Covenant on Harvest.
Halo doesn't glorify the SPARTAN program nor does it criticize the Covenant. The individiual races of the Covenant were even given personalities in Halo 2 and you truly learned their ways when the High Prophets ordered the executions of High Ranking Elites soldiers and initiated the Changing of the Guard, giving the Brutes, the hulking tribal warriors of the Covenant who follow the religion more devoutly than any other of the Covenant's races, the reigns as the Prophet's Honor Guard. The Grunts are just as blind as the Brutes, but cowardly. The Jackals as bloodthirsty mercenaries who follow the Covenant's religion so the Prophets won't eradicate their race. The Elites prove to be the best of the Covenant when they realize the error of their ways and break away from the Covenant in Halo 2 in the Covenant Civil War.
Bob, I understand where you are getting this Pure Race Vs. Diverse Group War you are talking about, but using Halo Reach as an example of this is a hard sell, because even though Reach is a prequel to the series, it provides a unique perspective in that Reach is invaded, overrun, and glassed without any rationalization given to humanity by the alien invaders. Earth and it's colonies are in the dark until The Pillar of Autumn and Master Chief John-117 land on Halo Installation 04 after escaping the doomed Reach. In my opinion, the bulk of the story is elaborated in Halo 2. Sure many of the little details are found here and there around the expanded universe of the Halo franchise. But I don't think it's fair to look at one specific part of the series and judge the entire universe established within it on it.
With all of that being said, I enjoy the new show and look forward to future topics.