No one said anything about making racism the point of anything. However, one would hope that in what ostensibly aspires to be a serious, somber narrative the topic would be treated as more than a cartoon shamelessly paraded for shock value. The inclusion doesn't say anything or add anything of value to the narrative.
Racism is not the point of the narrative, but it's not "a cartoon shamelessly paraded for shock value," either. Racism -does- add to the narrative here -- its pervasiveness in Columbia is reinforced by one man's rationalization of his treatment of others, rationalization he achieves through ideology. And this, in turn, is a subset of the game's true theme, which is how we as individuals and as a society deal with cognitive dissonance, and the consequences of both confronting it (Booker) or withdrawing from it (Comstock).
Think of The Searchers and Taxi Driver and how the main characters' prejudices colored their actions and motivations. Subtly alluded to but never face to face with a caricature of a big-lipped Sambo. Booker's redemption rings a bit false when fighting against such hilariously evil enemies. By contrast he doesn't seem like such a bad guy. Obviously he's done some awful things but at least he isn't Sky Hitler.
Booker doesn't seem like such a bad guy? It turns out he -is- the bad guy -- Comstock is his alternate self. Comstock is the Booker who chose to rationalize away his wrongdoing through ideology, and he serves to show the perils of absolution through ideology, how it enabled him to do even worse things, not the least of which includes perpetuating a society based on minority oppression. Let's not forget, Comstock was a "Sky Hitler" in the making, trying to bring about a future where a sinful America was smote from the Earth. He was now rationalizing genocide.
And then the Booker we play is the Booker who took the more nihilistic view of thinking himself irredeemable for the massacre he committed at Wounded Knee. Refusing to rationalize away his wrongdoing had its own destructive consequences -- namely, a spiral of depression, drinking and debt that culminated in him selling his own daughter. Again, the point of the game is, and remains, not issues of racism, and thus those issues were not undercooked; rather, they served the intended point of illustrating -some- of the consequences of whitewashing the past.
As far as cognitive dissonance goes, I agree, but I don't think it really works. It might have if anything before the raffle communicated to the player that Columbia was anything other than a terrible place. Despite it's colorful and cheerful palette, the setting is immediately creepy and off-putting with all sorts of cultish, Stepford vibes. Getting the chance to stone minorities only confirms it's a den of evil. If Columbia had seemed at all inviting or alluring beforehand, the provocative racial imagery might have caused a conflict to how the players felt.
I think you're in the minority thinking Columbia didn't seem idyllic at the start of the game. I suspect many people found the intro to Columbia to be magical. I know I got swept up taking in the sights and sounds, soaking up what felt to me like Heaven on Earth. It really seems like the perfect place. And that's why the stoning at the raffle is so effective; it's absolutely meant to be shocking and jarring, because the point is to establish the bigotry that exists in this society.
It's not even cartoonish: In real life, delicate ladies in sun-dresses would sip lemonade at a picnic on a bright sunny day -- as a black man swung from a noose overhead. This shit happened in America. Infinite's depiction of a biracial couple being rolled out to a jeering, bloodthirsty crowd seems tame compared to the real deal. So I hardly think they were heavy-handed in their approach.
Furthermore, they could've left matters at this scene and it would've been enough to establish the sort of society you're exploring, but scenes like the civil rights group with the Negro printing presses were there to also establish that not -everyone- is so bigoted, and that there are in fact progressives in Columbia, which I thought did an excellent job of making its world seem like a more real and well-rounded place.
Of course, the beauty is that all of these details are secondary to the tale of Booker himself. In the end, the bits and pieces of racism here and there simply add to Columbia as a monument to Booker's sin -- a vivid symbol for where society goes when it uses ideology to excuse its own actions.