One of the things I like most about BSG is its ability to be controversial. Most of the good guys have indulged in despicable behavior from time to time, and this but shows their humanity.
Here, no one is exempt from blame. On the one hand there are those who would commit genocide. On the other is Helo, who does behave like a traitor in the truest sense of word. What the episode does (though it should've been done better) is examine the moral question of whether treason is justifiable in the face of a greater evil. Indeed some would say that the true patriots are those "traitors" who work against wrong wars, like we're seeing in our own society currently. It's very much an open question with no clear answer, and the episode does overall a good job of presenting it this way. When TV shows are mostly designed for couch potatoes to get cheap thrills and quick satisfaction, a show with more questions and fewer answers cannot but be welcome!
What does bother me--and this has bothered me since the very beginning--is the lack of insight into the REAL philosophical question in BSG: what tells a Cylon apart from a human? Characters keep trading jabs about how "human" the Cylons are or aren't, but no real argument is ever made either way. Helo and Lee come close in this episode when Helo says the extermination of the Cylons is "a crime against humanity" and Lee responds that "they're not human: they're programmed." Well, aren't humans programmed also? Are we not also brain machines with wiring and chemical reactions? What do the Cylons have that we do not? Surely not some mechanical interface like a Borg implant from Star Trek, or else it would have been very easy to determine who is or isn't a Cylon. But then what, and what exactly *does* make them different?
At this point, all evidence points to the conclusion that there really isn't any substantial difference between humans and Cylons, and I believe that's where the series will end up going. The whole religious deal (Gods vs. God, creation, fate, the birth of a new human-Cylon generation and "the shape of things to come") points to a rich and deep truth about the common origins of the species. Let's not forget humans are the Cylons' creators, hence, in a sense, "God." This, along with the "minority" five Cylon models of which we learn in this episode, is exactly what makes BSG the most exciting series I've ever seen.