Well, here we go again . . .
Very quickly, the policy of preemptively exterminating non-combatants during the war seems no less irrational than a policy of preemptively exterminating all non-doctors during the outbreak of a plague: "Well, your average soldier doesn't know a damn thing about cell biology, so he's useless in the fight against this disease (except maybe as a test subject). They're not pulling their weight in the war against the plague, and that's unacceptable! So we might as well exterminate them and everyone else who isn't a medical researcher before they have a chance to become vectors for the plague." That seems to defeat the whole point of having doctors; similarly, having your soldiers exterminate your own civilians seems to defeat the whole point of having soldiers.
Not really. The purpose of having Soldiers, is to ensure the survival of the state. Not the survival of it's citizens.
I'm not here to protect noncombatants. I'm here to kill Reapers. See what I'm getting at? You can always make more citizens with the surviving Soldiers. This probably comes from a different perspective of Soldiers. I, as a Soldier, have no interest in protecting the American people. I'll say it. I didn't join to serve. I joined for entirely selfish reasons that center around me. But that's only a partial part of the argument. To me, the point of Soldiers in the war is to kill the Reapers. Much as the same in your next example.
That said, that actually makes sense. Kill the food, the plague has no way to spread. It's perfectly logical to me. It's like the Halo's in, well, Halo. Starve the flood by killing everyone. The flood all die and you repopulate the galaxy with the survivors. As I said above about the Soldiers, the point of Doctors and medical researchers isn't to heal the sick. It's to kill the plague. Stopping the plague is more important than protecting or healing the people who have it. Stopping the Reapers is more important than protecting people (namely, the people who are of no economic value to your effort). Don't kill everyone of course. You need to categorize people on what skills they have and what use they are to both the war effort and to rebuilding society. People with actual valuable and technical abilities such as architecture, engineering, horticulture, etc. (I'm assuming you get what I mean) are the people who are prioritized for survival, while the more extraneous ones in the positions that aren't so valuable or necessary to the continuity of civilization or of the race for that matter (no offense to you, but philosophers, painters, writers, liberal artists, etc. don't have any technical valuable skill to give to society when you look at it. There will always be more philosophers, whereas if you lose the few plumbers, you're kinda screwed in that department. That's not to say that they'll all die, but they tend to have less of an actual physical utility).
It's the litmus test given in KotOR to an extent, the one on Kashyyyk; You, the general, have the opportunity to destroy the enemies army. Doing so would mean putting your city in the path of their invasion and lead to massive civilian casualties. You have several options available; hold your army back and let the city be destroyed while you trash the headquarters element of their military (sending them into chaos), reinforce and protect the city, letting the enemy know that you are aware of their weakness, causing them to withdraw, but at the cost of drawing the war out, evacuating the city (an ideal option, except that you can't evacuate that many people without the enemy getting fuzzy to what's going on), or attacking the enemy head on and risking your own force to actively protect the city. Granted, you aren't attacking your own city, but the implication is that holding out will decisively end your opponents war prospects completely.
The military doesn't operate on litmus tests, and neither do Government agencies. To the former, all they care about is PT scores. To the latter, they care about connections, a language degree, and how much of a conservative WASP you are. And I wish I could say I'm exaggerating, but I am being dead serious about both of these.