The quarians came up with an effective measure to fight the geth, one that pushed the geth all the way back to Rannoch and threatened to wipe them out completely.
The Reaper signal didn't just render the geth immune to this measure, but put them under Reaper control "Is sumission not preferable to extinction"? The geth decided the answer was "yes" LEgion admits it.
And Reapers are created by murdering millions of organics and pouring them into a Reaper shell. You think no one in all the thousands of cycles had a problem with that?
Is a calm institutionalized genocide somehow "better" than an irrational war?
Until they faced extinction, only about 5% of the geth turned Heretic.
Who cares what the geth think of us in a thousand years, as long as they sty in their Dyson Sphere and spend their days calculating pi? We have nothing they want, they have nothing we want.
The Metacon War was fought against the zha'til, the "geth of my cycle" which were subverted by the Reapers. That whole war is invalid as far the the Reaper argument goes, since it was instigated by them to begin with.
Oh, well that perfectly validates the Reaper argument about the "inevitability" of war between organics and synthetics 
No option is valid. The entire premise is organics and synthetics are incapable of coexisting:
Destroy: organics exterminate all synthetics
Control: organics are forever dominated by synthetics (the Reapers)
Synthesis: Everyone is forced to change who and what they are a the genetic and even molecular level to meet some arbitrary definition of "perfection" or face annihilation. Implications unpleasant....
Conflict happens. War happens. You can't just program everybody to play nice. Not without subverting free will.
Putting them under Reaper control didn't change how much they had advanced and evovled up to that point. It didn't change the fact the Geth Dreadnought was tearing the Quarian Fleet a new butt hole. It did change the fact that the Quarian weapon was rendered ineffective against them. Which removed the one advantage the Quarians had for a successful attack.
Doesn't matter what they think. You honestly think that steak you are eating came from a cow who dreamed since they day they were born to be fattened up and then slaughtered so you could have a steak? Or that bannana who wanted to grow nice and big just to be cut from the tree, transported to a store to sit on display, taken home then left to rot on the counter top before being thrown away? You really don't understand the hypocrisy of you complaining about what the Reapers do compared to what we do.
Murder is Murder. Death is Death. Reapers murder because the AI says so. Solders murder because their commanders say so. Each rationalize their actions in their own ways. But either way it involves murder and death to further their goals. To do what they perceive as right and for the betterment of their culture, country, planet, galaxy.
That 5% of the Geth were able to steam roll all over the Citadel Fleet. Even taking out or nearly taking out the Desnity Ascension which was the largest and most powerful ship created in that cycle. Remember Sovereign basically ignored everything and headed right for the citadel. Only destorying any ship that was stupid enough to get in it's way by sheer blunt impact of hitting it.
It matters because organic's will worry. They will fear the Geth are advancing to much. they will try to interfear which will cause the Geth to react. Then there is the fact there are people who will try to replicate the Geth. Just because one version is willing to be at peace as long as they are left alone. Doesn't mean the next version will do the same.
The Metacon War was not against the Zah'til. They stopped the Zah'til by causing the sun to go super nova killing them all off. It was pretty clear it was early in the Prothean Empire that they encountered it. They forcibly united all advanced civilizations under their banner. According to Javik over time all species came to see themselves as Prothean. Hence why it is stated in ME1 that it was odd that the Protheans seemed to be the only space faring species of that time. Like wise it is well known the Reapers hit the Citadel first. Crippling the Empire. The Zah'til couldn't have been the cause of the Metacon War. How ever yes when the Reapers invaded they used them as pawns much like they did with the rest of the species.
Yes it does because difference is the biggest cause of conflict. And you can't get much different then an organic being or a completely synthetic being.
Your list of the options are funny.
Destroy only kills existing synthetics. Not anymore that could and would be developed in the future. Which would have developed anyways. So hat doesn't solve the eventual problem that will develop again
Control very clearly states that the new Shep AI will simply act as a guardian to all species. Not directly controlling them at all or putting them at it's mercy. Considering Peace is established oh so often by one group being stronger then the other. An AI with control of an entire Reaper army would allow him to put the pressure necessary to keep wars from breaking out. Which you know is exactly how the Council works anyways.
Synthesis no one changes who they are. Simply how they are made. It isn't an arbitrary concept of perfection. The change isn't to make you perfect is is to bridge the gap between synthetic and organic beings. There isn't any mention of perfection any were in the AI's description.
Conflict does happen. How ever the key reason for conflict is misunderstanding. If everyone understands each other the chance for conflict is severely reduced. You are literally pulling the Free will statement out of thin air to validate your claim when free will was never something that was under effect.
The entire reason the Geth and Quarians started a War was a lack of understanding between the two.