Well, it should be no surprise that there isn't one part of this response I find even remotely persuasive. I don't see the relevance of your personal reasons for joining the military to the issues at hand. What matters is the criteria you will be evaluated on by your superiors. Even if my only reason for becoming a doctor was to make money, and I don't care at all if any of my patients live or die, the fact is that if I allow enough patients to die that could have been saved with more effort on my part, I'm a bad doctor and will be evaluated as such by the community of my peers. Similarly with soldiers: Even if you don't care about civilians, if you actively kill millions of them, your actions are contrary to the general good, the good of the state and even the good of the army itself; to begin with, you'll be undermining the morale of your own soldiers (this is familiar territory, but it seems to bear repeating here).
From my point of view, what you say about the virus example makes little to no sense. Killing the plague is not an action that has any intrinsic worth; it's only a worthwhile task insofar as it's a threat to actual human beings; if you don't think that human beings have any value, then why bother trying to cure it? The most sensible thing would be to simply stay away from infected areas. I see things similarly with regards to the state. A state is a socially constructed institution that has no intrinsic value over and above the value of its citizens. The reason to act in defense of the state is precisely that the state serves the people; a state that serves only the interests of those few who are entrenched in positions of power is a failed state. If this weren't so, then we'd have to say that North Korea is an extremely well-run country because look how well the Kims have done for themselves, or that the DRC is doing pretty well because Joseph Kabila keeps winning elections.
As far as 'categorizing' people according to their worth, I'll just say that I'm skeptical that there can be a state apparatus competent enough to do something like this without causing more harm than good.
I think what this is going to come down to is a matter of how we place our values in something. In the context of the Reaper War, I judge them as a threat to myself and the few I care about, and a threat to my own machinations of power that I'd like to bring forward. I also have the ability to rise above the judgement and value from my peers into a near literal ascent into godhood. As far as morale goes, it's a question of how to make them fight. I think we got into that debate? You addressed several points rapidfire and I'm going to address them all as I can. I don't see how actively killing civilians is a badness to the state. I don't think we'd agree on general good (or we might, but we'd likely disagree on how to achieve it, and what achieving it is). As for morale, as I said, we've gone down that road. How is my army going to fight the Reapers? I'll ask that, because I don't believe the conventional motivations are going to cut it for them. But they're too engrossed in things that I perceive as a hindrance to the war effort. They fight for their families? Great. To me, their families are a taxing strain on my resources. What am I to do? Keep the family alive in exchange for their loyalty and performance (that I'm personally not impressed with) while having the family continue to draw resources from my reserves, thus limiting my ability to fight (while also giving the Reapers a potential source of new enemies/spies/saboteurs to use against me, with the benefit that while they attack them, they won't be attacking my forces)? Or destroy the family and risk losing the loyalty and performance of said soldiers while not being a burden on my overtaxed resources (and denying the Reapers enemy troops/spies/saboteurs while also meaning that they're going to be more direct in their attacks)? Either way, I perceive myself as being in a very disadvantaged position. Personally, I view it as a possible catch-22, but I believe in my second option. Or perhaps you can give me a third option. It's why I support Cerberus methods in ME3. It's damn brilliant to implant your army to be absolutely obedient to last. To do what I say, when I say, and how I say to do it. What I have is a quandary. Because I don't have that. In a circumstance as it is (or that I might hypothetically have) I don't believe I have enough to accomplish what needs to be accomplished with the army that I have. This comes down to what I believe Soldiers are; They're killers. When the chips are down in a circumstance like the Reapers, they need to ditch their humanity. Their compassion. Their identity. They need to become a machine that exists with one purpose, and with only one way to end that purpose. I expect my argument will bounce off ineffectually (not that I'm dismissing or criticizing of insulting you). Yours bounced off ineffectually quite ineffectually as well.
Here's the general strawman that I've thought a bit about. It's not that I don't value people at all. That's the first thing that I'll see as a mistake to interpretations to my philosophy (even possibly contradicting statements about them at all). I do value them, but I value my idea of what I think they could be, and what I think they should be. I value people in a way that you might find incredibly strange and illogical, just as I view the modern view of people today in the same light. I don't agree with or like what they are. I think it should be changed. Next, I'll state why I defend the state: You have the people; they just haven't been born yet. This is going to be abstract, and without a doubt you'll find it just as persuasive as my last statement. I defend the future. The the actual physical future. The physical, tangible reality of a future that can be built back up to trillions of people even if barely ten-thousand survive. I do defend the state out of my needs for it as well. And I think that even with the historical precedence that is given with your examples, all the Caligula's and Kim's to exist with the power to define the states alone, I do believe that there are those who can wield that power without being a Caligula or any Emperor in a Chinese Dynasty, or Melgarejo, Robert Mugabe, or Ceausescu. I do believe that all the power can be vested individually in one exceptional person and that that one person can rule the state to his own ideals with complete control as he sees fit and do a better job than anyone else.
And on that last note, it could be, but I'd ask how you'd find it harmful and whether we view that harm in a same light.