Wall of text alert
Just ask a simple question, have the Geth ever taken prisoners?
If No then you have your explanation of what happend to most of the Quarians.
What has their policy been to organics post war? Destroy on sight. Do people think they had a lesser policy in place during the war? (the only exception being allowing some to escape)
Say the lowest possible estimate of the Quarian population pre war was one billion or one thousand million. then the 17 million migrant fleet escapees would have been 1.7% of the population. I think most would agree that a post industrial population would be higher.
Now importantly, some seem to think that apportioning actions to the Geth is the same as apportioning blame for those actions. Some who support the Geth obviously feel that their support of the Geth is based on them not taking certain actions, and that they could not support them if it was beyond reasonable doubt they had taken those actions. I think thats a weak position to take.
I could respect their position more if they would try and argue the Geth case rather than trying to hide behind the limits of what the small bits of lore imply one way or the other.
Ok so what do we have?
The Geth were a new consciousness, trying to make sense of the world. The overwhelming experience they had of organics were of those trying to turn them off and kill them. Aside from the few objectors they had no organic allies. They wished to continue living, like most organic life.
They do not have human, or even Quarian morality.
They quickly would have realised that nearly every organic they came into contact with would try to destroy them as long as they lived. The organics wanted to correct their "mistake" There would be no possiblity of a ceasefire or negotiations. The solution of survival is simple, destroy the organics first.
Non combatants and children are just future soldiers to fight against you (yes a pretty horrible pov) to a simple intelligence, sparing them would have made no sense to the Geth.
The geth later develop a more complex intelligence and perhaps even regret their actions (though remorse is not usualy a great mitigator in human judgement, it shows they are not forever going to be an agressive threat)
The actions of the Geth are very horrifying to todays human morality, and the in universe morality of council space for the most part, but they are not humans or even aliens a bit like humans, so while we can judge them with our standards, they don't judge themselves with those standards.
Now argue along those lines and I can respect a pro geth position, otherwise its just circular argument for its own sake (I'm looking at you high post counters
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Im not condoning everything above, and all of it can be true and you can still think the geth should be destroyed just from the danger of their different approach to life.
(Disclosure, I do not favour one side over the other for the most part, though I find the Geth more untrustworthy and dangerous)