1.) Jesus.
2.) Christianity killed Greek philosophy, Greek scientific theory, Greco-Roman culture, and IMO aided the downfall of the Roman Empire. Enter about 900 years of superstitious faith-mongering and living in squalid conditions, with the occasional troupe of people heading east to commit some mass murder. Then, after all that ended, the persecution and religious wars began. Only since the nineteenth century has Christianity receded into the background as an instigator of violence and misery, and then only because it was replaced with ideals like nationalism, socialism and, later, national socialism. No Christianity = much, much less religious violence. (Please direct any discussion on this topic to PMs, let's not clutter up this thread, ok?)
3.) Quickly and without any witnesses, preferably before he got a messiah complex. Maybe drop a rock on his head or something.