I personally don't think that you can compare the Rachni, the Krogan or even the Geth with the Reapers in terms of destructive power. The latters simply play in another league. They steamrolled the whole galaxy within months without even really trying.
You can sign all the treaties you want, no nation/race/organization would accept such powerful beings as a neighbors. It has nothing to do with public opinions which you can manipulate with ease. Strategically, the very idea of someone being so much overpowered that they could dictate the fate of the galaxy the way they see fit, even if they actually don't want to, would be simply unacceptable. Look at what's happening every day in the world.
This kind of gets away from my point though, which was to say, we have been given the option to resolve conflict with synthetic forms of life in multiple ways. So, if from the story perspective (which the person I responded to was invoking), limiting the options to genocide or enslavement of them and having no peace option at all is actually less thematically in-line with the narrative than what we did get.
If we really do care about storytelling, then the option to make peace with them should have existed, even if it did not lead to the desired end.
To me, the end-game decision is far more worthwhile than Rannoch as it relates to the question of organic/synthetic relations. It is easy for the player to tell the quarians they need to suck it up and get along -- the player does not empathize with their hard feelings, nor does the player share the mistrust/fear the quarians harbor for geth. What are geth to a soldier who hunts Reapers? Come game end, you are faced with the Catalyst/Reapers in a similar situation. Hard feelings? Check. Fear and mistrust? Check. Now you are feeling what the quarians felt with the geth. How willing are you to accept the same peace you subjected the quarians to?
Now what if geth were more numerous than all other space-faring species put together? What if unshackled EDI could take on Skynet-caliber power? Would we still happily have the quarians make peace with geth on Rannoch, or still defend and respect EDI's personal freedom? Nobody asks themselves those questions because, when you beat the game and turn off the console, you do not have to. And do not want to, since it might actually lend credence to the Catalyst's position (better to believe what you want than accept the truth of things, clearly).