The characters are shown as extremely loyal to their superiors rather than to an ultimate set of laws. This is suicidal for the Gallactica society because this sets up a society of anarchy.
I don't see anyone on either ship as being really evil in what they do. The two admirals plans to wipe each other out are based on their honest convictions. This also points out how useless their president is. She should have the power to make a decision one way or the other. One weakness of this show is that the president is highly reverred but does nothing to justify it in action. This leaves all the drama to the individual admirals or captains.