Completely agree with caspartine and pedrolago. I think the reason Geralt's killing of humans in the books feels so much more brutal than the killing in the games is because they're not just about killing. There is much more emphasis on character development and character interaction, which lends a lot more weight to those situations when Geralt does kill people. Similarly, I don't think it's just the animations that need to change in the games to change the player's perception of killing, but the entire implementation of combat - as caspartine put it, the '-1 enemy, +10 XP' mentality has to change, which probably means that the game would feature less killing (and, in the eyes of some, less gameplay).
However, I think it's more an interesting thought for now than something we'll actually see in TW3 - although CDPR don't seem afraid to deviate from industry tropes in general, I don't think this is what they're trying to do with the Witcher 3 just yet. But maybe, in a couple of years, we will see killing change from a simple gameplay mechanic to something which actually causes the player to feel empathy towards the characters in the game.