cjrgreen: If Geralt remains neutral, he allows atrocities to occur through his inaction
This is the mentality of the Grand Master. The Grand Master sought to avert great atrocities by means of lesser atrocities--"the ends justify the means."
There are, classically, two schools of ethics.
1. Utilitarian, or ends-justify-the-means. This is the Grand Master's stance, and it is a stance that would support Geralt taking sides.
2. Kantian, or, every action should be considered as an end in itself. Thus, killing is not an acceptable means to an end, because killing, as an end it itself, is obviously unethical.
cjrgreen, I think YOU would have made a better game (as far as the neutral/order/squirrel thing goes) than CDProjekt did. As it stands, neither the Order nor the Squirrels were clearly pursuing the greater good. If they were, the player's decision would be tougher--should I help terrorists (or racists) in the name of justice, or should I allow injustice to continue on the basis that a violent intervention would be unjust in itself? That should have been the decision for the player to make.