Even looking beyond the moral considerations, this whole idea of killing civilians before the Reapers can kill them just seems like a massive (no pun intended) waste. Let's say you're right that they confer no benefits for the war effort. The reason you don't kill them all is because of the costs associated with killing them. Even if you don't care about civilians, the soldiers you're giving orders to will. Having them actively kill their own civilians or even fail to act in their defense will quickly sap both their morale and their confidence in your leadership (indeed, the cumulative psychological effect of the billions of casualties caused by the Reapers is something ME3 is constantly trying to impress on us). So I just don't see the point, even from a purely utilitarian point of view.
Returning to the topic, I'm going to say something even more inflammatory than anything MassivelyEffective0730 has said: Ready? I think the most poorly written scene in the series was Tali's loyalty mission. *runs and hides*
That's a problem to deal with, and it scares me: That's why part of me completely agrees with the ideal of having Cerberus shock troops who will obey me without question or hesitation. If my own people don't have the will to be evil, to be monsters themselves, then how can I hope to pit them against Reapers and win. Yeah, I think the shock troops were a good idea, as long as they could be controlled. Absolute obedience is a must. I would question my troops on why they would have the confidence to follow me if I didn't have the capability to do what I needed to do. I wouldn't be worth following if I didn't. Either they don't have the package to do what I tell them, or I don't have the capability to win the war. Being a hero, being some kind of savior, it's not going to protect them against the Reapers. I'm not going to win, nor do I deserve to win being anything less than what I am. They need to steel themselves from compassion and humanity. They need to be just as machine-like and robotic as the Reapers they fight, if not more so. Hell, that's why I'd want a Clone Army from Star Wars, or a Droid Army, one of absolute competence, and one of absolute obedience. I'm a terrible leader if I can't trust them to do what I need them too, and I'm a terrible leader if I can't do what I need to do.
That's what I see as so beautiful about the Reapers. I admire them, and their singularity of purpose and will, and I wish on my hands and knees that my people were like that. To make a few quotes:
'And I thought: My God... the genius of that. The genius. The will to do that. Perfect, genuine, complete, crystalline, pure. And then I realized they were stronger than we.'
- Colonel Kurtz, Apocalypse Now!
Master Payne: For all we know, those are some new form of revenant, and the only thing to do is kill them. Could you burn down people — women and children — even if you knew they had become monsters?
Agatha: I ... No ... I don't know.
Master Payne: The Baron can. The Baron has. I respect him for that, but I don't want to be him.
- Girl Genius
"You still don't understand what you're dealing with, do you? Perfect organism. Its structural perfection is matched only by its hostility. I admire its purity. A survivor... unclouded by conscience, remorse, or delusions of morality."
— Ash, Alien