Whilst not suggesting that the methods used in slaughterhouses are in any way pleasant, I wonder whether it is linked to the standards that we seem to be willing to accept - to ensure cheap food - whilst the animals are alive? If these were better, would we not tend to treat them better at the time of their slaughter?
Mind you, I suspect that the means of slaughter are streets ahead than those used by our ancestors - spears, arrows, clubs, etc.