They were AI not VIs. That were transformed into borg from Star Trek like creatures. At least I pictured the borg when I heard about them. Something we see the Illusive Man repeat in Project Overlord.
Leviathans still consider the intelligence to be doing their bidding. It is preserving organic life at all costs. Reapers are more then capable of annihilating any and all species in a matter of moments. You continue on this line of reasoning that they are killing because they like to kill. Yet you ignore how easily it would be for them to take out species quickly. A tungsten rod the size of a telephone poll fired at near the speed of light would result in massive damage on impact. Shepard wouldn't even have time to get to the Normandy if the Reapers wanted everyone dead. The game would have just been a 20 second video of Shepherd walking to the council office then being killed along with everyone else in the city thanks to 1 shot from any reaper.
Also remember the Leviathans quiet literally controlled the entire known galaxy. Every new race they encountered they would enthrall to their will. The concept that one of their tools might rebel against them was unfathomable. It is like us expecting house cats to rebel against us. We just can't see it happening so we don't plan or think about it at all. So when they do it will be completely by surprise and almost all if not all of us will be dead before we could react. They don't manipulate evolution they only lay the ground work for civilizations to develop once they reach a certain point. Protheans manipulated species far more then it does. Remember they didn't initially start the 50,000 year cycle. That set up was created later. Evolution is the key. They evolve, create their own societies then once they reach a certain point the intelligence gives them the technology needed to speed up the development that might normally take 100,000 years on their own. And it lines up about right considering only 300 years before the harvest would normally take place the Quarians feel into the same trap as countless species before them. The creation of a synthetic race that started a war with the survival of the Quarian race at stake. Then later the Quarians attack the Geth again. Only surviving (if you picked them over geth or both) because Sheapard intervened.
Even without Sovereign's actions the Quarains would have attacked the geth. Lost and that would have drawn the council into it. Igniting a galaxy wide fight. And I can say lost without a doubt because it is the actions of Sovereign that expanded the geth thus gave Quarian's like Tali more access to their tech. Along with any upgrades picked up thanks to reapers to them. Which allowed them to be successful against them in ME3.
This is the cycle the intelligence wishes to break to preserve organic life at all cost. It isn't necessarily just synthetics rebelling against organics. But organics creating perfection then being frightened by what it can do and reacting by attacking it. Causing the synthetics to fight back to live and in many cases kill off their creators.
And I will repeat what I said above that you ignored:
Destroy simply removes the existing group of synthetics. Reapers, geth, EDI all gone for now. But newer ones could take their place. Particularly if geth are gained as allies reducing the stigma behind creating AI. Thus allowing it to happen again.
Control simply puts all synthetics under one group mind. Reapers, geth, EDI all lose what made them individuals to be controlled by a central AI. Much in the way EDI controls the Normandy and Dr. Eve's body. If the reapers harvesting humans to create a centralized intelligence that represents them is a bad thing. Then why is it a good thing to be done to AI's?
Synthesis provides the best part of each to the other. Thus breaking down the barriers that have divided organic and synthetic and the reason the cycle of war has repeated over and over again. That is why the catalyst favors it. Because that option is the one that for fill it's programming by making it so organic and synthetic won't fight. Preserving organic life despite synthetic life's continual advancement.
Because the fact is synthetic will always surpass organic. So how do you keep the balance?