Haven't seen you framing it as "them or survival" so much as "them or inconvenience." The galaxy isn't populated by lobotomized Cerberus drones who would turn their weapons on their own families without question to eke a big closer to a 100% efficient war economy (never mind the drain on resources that such an extermination would itself represent (looking past the moral horror of the holocaust (I know), try thinking solely of the trains, weapons, personnel etc. devoted to it which could have been deployed to the front) or the difficulty this adds to post-war recovery). There's no point in musing about what could be accomplished with an army of drones unencumbered by morality or free will when what's available is a multi-species force mostly composed of individuals with families they hope to see survive the war. Morale remains a key factor to success with such an army.
...on an off-note, can Cerberus drones conceivably reproduce? If they were all that remained of humanity after the war, would there ever be a "normal" (non-cyborg) generation of humans again?
That sucks then. Hell, part of me wants to see the galaxy fall. It purges the weak. Thinking about it, there's not much to the holocaust that could have been conceivably added to the German war machine: they were rather efficient with how they killed. The sublimation of metal pellets into gas was a rapid means of killing people off.
Said multi-species force doesn't deserve victory. I have no faith in their ability to win. I want them to fail. I want them to see how puny and futile their efforts are. I want them to be broken. That way, they can be born anew of something far stronger, far more powerful, and far greater. My Shepard says it in no uncertain terms: Be willing to die. Give up hope. It's the only hope you have.
I take the Lt. Col. Spiers approach to conflict (because I've seen first-hand how devastating it is compared to the opposite method). You can have the idealist, Harry Potter-esque version, which is the ideal that you fight because you have something to lose, or something to gain.
And then you have the cynical, and (in my opinion, and based on my observation) the more effective method, which is where you fight because you have nothing to lose. Your back's to a wall. You have no hope of survival. Give up any hope of survival. Give up hope period. Soldiers who gave up hope also gave up fear. There's no point in being afraid. There's nothing holding you back now. It's a kind of bitter irony: accepting that there is no hope for you, accepting that you're nothing more than a killing machine who's only mortal purpose is to be the most effective tool possible is the only thing that might save you in the end. It turns off the human part of you. Humanity is an intrinsic part of the psyche that must be purged in war. It's why I find the Reapers oddly beautiful in how they act. It is indeed perfection.
We must become something more than them. Hell, if my Shepard picked control, he'd continue the harvest until only those strong enough to overcome their weakness remained.
It's probably why I'm so partial to the Clone Army and the Droid Army in Star Wars. They won't stop until they win, or they're dead. The only two things in war that should ever matter.
As for the future of humanity post-war? Who know. I would claim who cares? If we just go back to what we were before, I'd consider my efforts to be a hopeless failure. If I knew that humanity would fall back into what it was before, I'd let the Reapers purge us and be done with it.