If BSG has its own sub-genres, one of those genres is the Star Trek-style morality play. "Downloaded" comes to mind. It might be worth noting, however, that the Star Trek characters didn't contemplate genocide the way the human characters in BSG are willing to.
Or, come to think of it, maybe they did. TNG's "I, Borg" contemplated the possible destruction of the entire Borg race in a way similar to how "A Measure of Salvation" here contemplates the possible destruction of the entire Cylon race. I guess the difference is that the characters in "I, Borg" couldn't go through with it, whereas the characters in "A Measure of Salvation" can. Or at least many of the characters can. They don't all agree, which is a promising point for drama.
The Galactica crew investigates the crippled Cylon basestar encountered at the end of "Torn" and discover that the entire Cylon crew has been infected by a deadly virus. The Colonial Raptors return with a number of surviving prisoners shortly before the basestar self-destructs. It turns out that humans are immune to the virus because it is similar to an ancient human disease. Sharon (whose new call sign is Athena in order to differentiate her from Boomer while throwing a nod to the original series) is also immune because of antibodies she developed while carrying her half-human child.
Dr. Cottle cannot cure the Cylons but says he can treat them with medication that will keep them from dying. The Cylons are afraid of what this virus could do to them collectively, so perhaps this treatment can be used to leverage information from the prisoners. Lee comes up with a more sinister plan: Stage a battle, and when a Cylon fleet with a resurrection ship comes nearby, execute the prisoners, and the disease will be uploaded into the resurrection ship and spread into the Cylon population, possibly wiping all of them out.
Okay. First some words on the technical details of the plot before I deal with the moral implications. I guess I simply don't understand how the resurrection ship works.
(1) Just what is this ship's range? In previous episodes, there was plenty of reason to believe it was quite a ways — certainly far enough to transcend one or more FTL jumps. If, for example, Boomer could be killed on Galactica with no Cylon ships nearby and still be resurrected, why doesn't the resurrection ship's receiving range reach the Galactica's present position? Why does the Galactica have to jump within engagement range?
(2) Wouldn't the resurrection ship have some sort of virus protection program? Why wouldn't it detect the problem with the incoming Cylon downloads and terminate the process?
(3) If Sharon is immune to the virus, couldn't the Cylons, with all their superior biological technology (they have taken human form after all) manufacture the antibodies to cure themselves?
(4) Since when is the resurrection ship a transmitter in addition to a receiver? If the virus is replicated in the downloading process, why would it spread beyond the resurrection ship? Why can't the Cylons simply quarantine the ship? Why would it spread through the whole population? (I suppose the Cylons don't have an adequate firewall either.) If the Cylons are so heavily networked, why do they need a special resurrection ship in the first place?
Suffice it to say, the whole downloading process of the Cylons strains credulity. I've accepted it in the past because it hasn't gotten so detailed, but now we have a plot that's based upon the tech, and I don't think it holds water. The more the downloading process is explained, the less I want to hear it. (Although I'm still awaiting the answer to how a Cylon is downloaded if it's blown to bits and the brain that houses its memories is completely destroyed. Where do those memories go until they're retrieved?)
I suppose the simple answers to all these questions are that, yes, the resurrection ship is a wildly implausible device, and, no, we shouldn't try to come up with answers for why it would or wouldn't work and instead concentrate on the moral implications. Fine; I'm willing to do that, because such questions are what make this an interesting episode. Lee's plan is quickly commissioned and put into action. The biggest voice against this plan is Helo's, who argues that genocide, even against machines, is simply wrong, despite what the Cylons have already done to us. If we do to them what they did to us, a piece of our own humanity is forever compromised.
He has a point, despite the fact that at times he also comes across as a Cylon apologist with a biased viewpoint and a Cylon wife. One of the strengths of the episode is how it puts up convincing arguments for both sides.
Even Adama is not sold on the morality of the plan. As a pragmatic military decision it's certainly the right one, but as a moral decision, he clearly doesn't want to have to make that call. Who would? That's a responsibility that shouldn't have to be anyone's. Roslin makes the call, and we sense that her experience in the "snake pit" of New Caprica plays a role in her attitudes here to destroy as many Cylons as possible. She has her own convincing points: The Cylons have already tried to destroy us all, and they still show no signs of stopping. This is particularly clear in light of the fact that everyone now knows Baltar is still alive and helping the Cylons find the path to Earth.
I found Sharon's personal stake in her people's possible demise somewhat touching, and found it especially interesting that even with that knowledge she remains steadfast in her determination to maintain her allegiance to the Galactica and its crew. She chose to be a human being, and that's a promise she intends to keep. If she's ordered to help destroy the Cylons, she will help destroy the Cylons. She won't like it, but she will do it in order to prove which side she's on.
Aboard the basestar, Baltar is found out for covering up his discovery of the virus on the crippled ship in "Torn," so D'Anna tortures him to find out what he really knows and if he actually orchestrated a plot with Galactica. Of course he didn't, so he has nothing to confess, so the torture of Baltar is essentially trying to squeeze water from a dry sponge. To survive his ordeal, Baltar tries to focus on his visions of Six, which leads to a truly peculiar torture/sex scene that has the strangest juxtapositions of any such scene I can remember.
At first when I saw this scene I couldn't decide whether it was inventive, pretentious, or absurd. But the more I think about it the more I like it. This is the first scene I've seen that combines torture, imagined orgasms, religious debate, unanticipated questions of faith, and somehow comes together and seems to make sense even if we can't be sure exactly what's in the characters' heads. Watch D'Anna in this scene, and you see the torturer become the one who breaks because of what she believes she might be witnessing. It's a complicated and intriguing scene that doesn't show all its cards, but shows how D'Anna is willing to operate on faith.
Of course the Galactica's plot to wipe out the Cylons fails, as it must. It fails because a character makes a decision: Helo cuts off the oxygen to the prisoners' cell, killing them before Galactica jumps within range of the resurrection ship. A few questions about that: (1) Hasn't it been established that a resurrection ship has the range to download dead Cylons from one or more FTL jumps away? (2) Wasn't it established in "Downloaded" that dead Cylons could be downloaded hours after they were killed? (3) Shouldn't Helo be court-martialed for treason rather than having the incident swept quietly under the rug, despite what Adama might have personally felt about the plan?
The outcome of this episode at least shows a character making a big decision and taking a moral stand. I'm just not sure that this could happen without severe consequences. You can't run a military ship with officers openly defying the chain of command. Hell, "Torn" showed that just last week.
Still, for all its flaws — and they are notable — I'm recommending "A Measure of Salvation" for asking a tough question and sufficiently dramatizing it, even if it's a question that this series has become quite familiar with.