Baptism is obviously a huge trigger in this game. It signifies your entry into Columbia, and then later on your death and rebirth (simultaneously). It also shows the transfer of guilt in your life over past events and how that guilt is twisted by:
a) accepting the baptism
b) not accepting the baptism
The Booker DeWitt we played as did not accept the baptism, and in doing so dealt with the guilt of giving up Anna through a life of alcoholism and gambling. This leads Booker to the story we play...
The Booker DeWitt who did accept the baptism feels cleansed of the guilt of giving up Anna. However, with both Bookers having committed atrocities at Wounded Knee, this Booker is still dealing with this part of his tortured psyche.
In creating Columbia, a city where racism is rampant and blacks are told they should be grateful for slavery (hey, free food and shelter!), DeWitt has placed blacks at a level so low in the social hierarchy that they are practically animals. Dogs. And he can much better deal with the guilt of Wounded Knee if he sees his victims (non-whites) as far less than the noble humans he dictates his prophecies to in his city.
It makes the socio-political issues in the game both grander and more personal. It shows the makings of the man behind the madness, the reason for all of the misguided hate and prejudice. Both Bookers were destined to fight the Vox (the blacks) for very different reasons.