I firmly believe that what Kara Thrace did to Leoben in "Flesh and Bone" was wrong. I believe that a society which employs torture on the defenseless captives in its custody has crossed a bright shining line that civilized people should not cross. Likewise, I think that Laura Roslin promising a man freedom only to kill him in the end is abhorrent to the ways in which I want my president to behave. However, I also understand why each of them did what they did. I understand the emotional, psychological and moral quandries which can lead two moral, good people to take such ghastly actions. And, in the end, I also believe that it was true to who characters really are, and that trumps everything else.
There's much to like about the show. The unwillingness of its creators to pass clear judgment on the actions of its characters is part of what's makes it great. While "bad guys who are really good" (think NYPD Blue's Sipowicz) are a staple of episodic TV, the new Galactica benefits from not having clear heroes and anti-heroes. Not a perfect show, but nonetheless fairly unique in its willingness to embrace moral ambiguity to allow us to contemplate moral complexity.