In my opinion, with the limited background story given, I'm guessing that there was less of an issue of good vs. evil as much as unreconcilable differences caused by human gregarity and our islandlike nature.
It's just the very issue of 'cultural relativism' that Drath explained so eloquently. If you grow up in a society where it's 'ok' to shoot your neighbor if he does something you don't like, where force rules, and only the strong survive, you will not consider this wrong - you will consider this the nature of Everything.
Only when exposed to something different can you be different - otherwise, only in very rare circumstances do people deviate from the acceptable norms to achieve something that may be looked at from PR-0927's 'universal good' point of view as better.
And often times such people, divine or not, die on crosses.
So, in all probability, did the Advent get wronged in the past? Yes. Were they probably evil? Maybe or maybe not, but there was probably a better alternative. Are they wrong now in interposing the sins of the father onto the great-great-great...>x50... grandson? Definitely. Hopefully, if they DO beat the TEC in the end, they don't cast the people away into space. They'll just be dooming their own descendants, 1000 years down the road, to a senseless campaign of revenge.