You have a point Blunt, not evil because not human is a bit fishy. I would still support that the Nomads are not evil, however, I mean we humans invaded their space, defiled their birthright, and disturbed their sleep. What were they supposed to do?
The incident at Sol is assuredly a strange one, but perhaps the Nomads had been watching the war of the Alliance and the Coalition (I wouldn't be surprised) and deemed us not fit to survive? Think Battlestar Galactica for a second, that reason was good enough for the Cylons to enact comparable genocide.