Kotaku and Polygon missed the point on the violence in Bioshock in my opinion. Their point is that having excessive violence limits the audience needlessly. But the whole game is a critique of patriotism, tea party politics, American history, with racial and religious criticism as well. All of that limits audience massively.
The violence in Bioshock is just as "on message" as anything else in that game. American empire, racial injustice, all of these things were built on violence. Americans are always presented with a whitewashed version of war and violence, and I find it incredibly ironic to champion a game that tries to criticize that while still demanding that they whitewash it to make it more palatable.
At the end of the day, the goal should never be about maximizing audience unless you're a publisher. Difficulty, complexity, nuance, controversy all limit audience, but they also make things great. Levine's vision for the game clearly included graphic violence. One could even say it's about the violence that American empire projects coming homing to roost.