Jedi Master of Orion wrote...
If they achieved total military victory like it is implied they did, then going on to exterminate them was unnecessary. It couldn't have been that hard to destroy the threat they posed without wiping every last man, woman and child out. The reasons you mentioned are probably the reason why it happened, but just because they didn't know any better doesn't make it ok.
Considering they know better
now, and considering the Quarians acted the way they did
despite knowing better, they still come out far better. And besides, if you don't have a choice (not "I don't have a choice" as in "I find the other option inconvenient", but as in "There literally IS NOTHING ELSE"), you're not guilty, they didn't decide to be born, well, retarded, and more importantly: they grew out of it, there is no reason to punish them for something that they didn't begin and the end of which they couldn't influence (Except at the point where they eventually stopped after becoming capable of doing so). It's not "ok" in the sense that killing a lot of people is clearly not ok, but if there is literally no other option, possibly not even the option to just do nothing/get killed/kill yourself, because you're simply not capable of the necessary thought process, then you are NOT responsible, because responsibility requires choice. A human would be put away because s/he would remain a danger to society, but the Geth have since demonstrated that they have grown out of that state and no longer are such a danger.
You are arguing that you can't side with the Geth because they're not completely innocent (I might actually be inclined to say that they might be, although there are not enough details of the morning war and the state of the Geth at that time known to really decide about that), I'm arguing that you can't side with the Quarians because, no matter what the Geth did and whether they had a choice or not, the Quarians tried to do worse things, and
are still trying to.
The simple fact that the Quarians lost doesn't mean they deserve support when they try to repeat their past mistakes, or would you, if I (As a German) were to tell you today "Yeah, you know, my ancestors tried to kill all the Jews, but we lost, so I guess we get another shot", support me? Of course not, because I too would just try to finish a wrongdoing my ancestors started, just like the Quarians would if they tried again to wipe out the Geth.