They are guilty of war crimes, and as such deserve a fair trial whenever they are captured.
The danger is not in killing Cylons; the danger is in killing things that look human. We are _visual_ creatures, and it's easy to blur the line between "Cylon" and "that woman-looking thing over there".
I can toss out pithy sayings - "The ends don't justify the means", "when you act like the enemy, you become the enemy". They're pithy, but true. The object is to survive while keeping the moral/ethical/behavioral upper hand. Otherwise you get what I expected the episode to turn into: "We're from the Pegasus, we're better, and we can do whatever we want to both the Galactica crewmen and civilians because we're better". Classic pack behavior. And, from the comments of the drunk Pegasus crewmembers, it was about to come to that if the Sharon scene hadn't intervened.