It really makes no difference to the way things unfold - it's literally just a a couple of lines in the next dialog, and then the story converges back to the main line.
That's kind of the problem with the whole thing - you really are on a rail, and you have few places where your choices have a lasting effect on the outcome.
Don't take me wrong - I love the story, and I wish they would release more content like it. But the state of the game at the end is pretty much predestined.