I feel like the big dissonance came due to the fact that we were killing HUMAN beings.
In Bioshock 1, we KILLED thousands upon thousands of splicers, but no one raised this disonance issue.
I feel same holds true with columbia. If these were just mutants, none of these questions would be raised.
Which brings up the question, are games cornered to having enemies soley be mutants/zombies/monsterous creatures.
Or is there actual room for games to kill human (that isn't a war game)?
I mean it's funny..but in Indiana Jones, this guy killed hundreds of people throughout his treasure hunting adventure, and no one really bats an eye at that. I think it's due to the fact that people realize, it's a fictitious film, and that killing has to happen in some fashion, and really don't pay attention in that regard (similar to Infinite I guess)
I think it's more than just the fact that they're human. In Infinite Booker kills first. He doesn't know whats going to happen when they grab him at the raffle but he decides it's appropriate to jam a spinning hook in someones face. From there he only gets more brutal and the people of Columbia can be seen as defending against his attack for the most part. In Bioshock 1 except for the Big Daddies the enemy attacks first and attacking the Big Daddies gets justified. You're either rescuing the Little Sisters or selfishly harvesting them which negates the dissonance because you're no longer the good guy.
I think lots of games have handled it better. There's still the ridiculousness of one person taking out so many people but the enemies should always attack first. It also comes down to player motivation. If the story is calling you a hero but you're killing people for an unrelated goal or a conflicting goal that doesn't seem worth murdering over it's going to raise some red flags. You could just make the player character a bad guy who doesn't have a problem with murdering people which is what some people claim Infinite does but it's only explained after the fact. Even if on a subconscious level Booker knew who he was it doesn't matter because the dissonance is between the player and the story not the character and the story. Anyone could create dissonance by purposely playing the game with a different motivation but in this case the game gives you a dissonant motivation only to reveal it's withheld information from you.
The idea of Ludonarrative dissonance has been around for a while and has been pointed out in many games. The first Bioshock definitely had it's fair share of accusations. Ludo- comes from ludic which essential means play so it doesn't really apply to movies but there's a lot of criticism for similar ideas in film. When a character's actions don't gel with their motivation it sticks out.
Jon Blow: https://www.youtube.com/watch?v=mGTV8qLbBWE
EDIT: Sorry, I don't remember the timestamp, but I highly recommend this lecture if you enjoy commentaries on the medium itself (which many Bioshock fans seem to).
That's a really good lecture. He says something like "Forty years from now Bioshock won't be held up as one of the turning points in video game design...and if it is I hope I'm not in the industry anymore!" A lot of what Bioshock 1 and Infinite get praised for isn't really video game specific. Movie style narrative is already an art form of it's own. They're good games but they don't really do anything that separates them or pushes the medium forward the way a lot of people claim they do.