Slaughtering the conquered enemy was the exception, not the norm, at least throughout Eurasia with whose history I'm most familiar. Was that the norm in the Americas? Considering the negligible amounts of historical data preserved about many of civilisations there, can one even make such a sweeping conclusion? Even if that were the case, significantly more people lived in Eurasia so that would still be the exception for the generic human population.

It has nothing to do "western culture", but with the evolution of warfare from the "Cabinet wars" to nationalistic "total wars". Colonial wars were often with brutal consequences, but again, massively slaughtering the native population was the exception, not the norm ( Herero and Namaqua genocide). The vast majority of humans conquered in the last few centuries weren't slaughtered en masse for the sake of it.