I always saw the subtext as being more of a rage against conformity/obedience given that the Covenant kept reminding me of the Crusaders and that the elites (the enemies considered to be smart and creative in the army) were considered the good guys once they decided to stop blindly following orders whereas the Brutes (portrayed as the muscle-headed, simplistic, lumbering foes) were evil once they stepped up to this role.
On the other side of the war, you have the Spartans, who are encouraged to find their own solutions to problems, who happen to live longer than the marines, who are even dumber than the Grunts and who seem to always look to you for every action they do. In addition, Master Chief blindly following orders was what almost destroyed the universe. Also, look at Foehammer, that pilot who kept helping you out in the first game. She says she's being tailed by enemies, yet never the less obeys the order to come and pick you up, leading to her death (and if you stay and watch like Cortana tells you to, there's a chance that you won't make it out in time). In Halo 2, you often see him pull off several plans of his own that get authorized rather than ordered that all seem to work, as opposed to several of the ordered missions that go awry. In Reach, all orders you get seem to only put you in danger or end with the death of a squad member. Reach itself is another big demonstration as well: the militarized planet that serves practically as a representation of Humanity's military is destroyed slowly with dependable items such as radar, evac vehicles, guns, ships, etc. taken out one by one. The final place to fall (other than the evacuation point) is a lab, a symbol of creative thinking. However, ODST provides the greatest example of them all: the jump. It almost brings up the old "would you jump off a bridge if everyone else did?" question that is used to counter stupid conformity, especially if you know about those pods and the fact that there is no real testing for either the jumper or the pod itself. Of course people playing without the knowledge don't really know this and brush off the completely warranted fear.
And then you have the Flood, parasites that eat the mind and that have a single hive mind (or operate blindly without one). These are considered to be the most evil of the three groups, as they not only overwrite life, but also knowledge itself (as seen by the corruption of Cortana and the infection of ships), despite the fact that this often leads to much more inferior results, all because they want everything to conform to their group.
This is the strong subtext I always got from the series, not some sort of subtle racism.
