Thing is, the Jews were a threat to Germany only in the twisted, paranoid rantings of Hitler and his deluded countrymen. The Cylons had already
wiped out upwards of 99.999% of the human race and were still attacking
. This wasn't genocide as a retaliatory act that Apollo was suggesting, Devil Eyes
, it was genocide as a necessary pre-condition of the human race's survival, the paranoid fantasy of genocide-as-self-defense made real. As such--within the logic and reality of the show
--it was the only tenable option unless the human race was willing, like the Halkans of "Mirror, Mirror," to die as a race in the name of a pacifistic ideal, a hard sell in a show predicated on militarism. Helo took it upon himself to make that decision and it was only the crude and arbitrary plot twists of the subsequent episodes that vindicated him. Were I Adama and/or Roslin, I'd have airlocked him.