The collapse of Y chromosome diversity around the transition to agriculture and civilisation is far from being exclusive to white or European culture. It happened in every human population that took up agriculture, to greater and lesser extent.
Violence is absolutely part of human nature. Serial killers are probably pathological but mass murder is definitely within normal human behaviour. The Mongols were less especially brutal than especially organised, ditto for the Nazis at a later date.
Kill everybody and take their land is more or less what happened to both the Neanderthals and the first H. Sapiens in Europe. Kill all the men is practically a humanitarian innovation.