The lack of story choice - with the exception of Arthur's two big choices - was partly a result of bandwidth. We just didn't have enough level designers and animators to make small story choices.
However, it is key to the story that certain characters are terrible to certain other characters. Everyone in our world has been broken by the experiences they've had. If we let the player play these characters as less terrible, then that might come through intellectually, but maybe not emotionally.
To get back to Bioshock Infinite, it kind of lets you off the hook, doesn't it? You can throw the baseball at the announcer. But the truth of the situation is that lots of ordinary, decent people would throw the ball at the interracial couple, and then feel horrible about it, and then attempt to justify their actions to themselves for the next thirty years.
Our story is about memory and denial. Those have a terrible cost. If you felt uncomfortable, well, then you entered into that. Which is awesome, and thank you.