so, the morality of the choice is "by far the worst" (in your opinion) because it is doing what the Reapers were attempting to do for millennia.
But what if the Reapers are right?
Frankly I dont care if they are right. One thing pretty much all of humanity agrees on is that some things even if done for the right reasons or because they believed in what they were doing are still too horrible. The medical experiments by the nazi's and japanese during the war, moved our understanding of medicine much further, however they were still horrible war criminals.
And anyway, Reapers were doing it because they got stuck in a logic loop of their own making, I doubt Leviathans were very pleased when they started massacring them or the species that were under the leviathan control when they died. And anyway all those species that were harvested to create reapers, they dont live, they are imprisoned, dead, worse than dead because so little of them remains for the others to find.
I find it extremely likely that all those synthetics that were killing organics were the same as geth heretics, spurned on by the reapers to do their bidding. Manufacturing evidence of their own theory proving themselves right. And as we know reapers are controlled by an AI that could not look past the problem, its solution to the problem was incredibly flawed, nearly as bad as the problem that they manufactured themselves. So trusting it? Because it "might" be right? Considering what it has done over the millions of years? Considering it was stuck in a problem of its own creation? No. That would be foolish. It would also be a betrayal of the galaxy and the people in it. They fought to be themselves, they fought to have a right to live, to determine their own fate, forcing something like that on them is a betrayal of the same magnitude that the first Reapers did to Leviathan.
After all Leviathan created Reapers to act as a kind of gardeners for the organic species they had enslaved, they wanted them to safeguard the organics from the possible destruction at their own hand(creation of synthetics which were probably made to kill Leviathans in their attempts at rebellion) and yet what did the Reapers do? Slaughter every species high enough on technological ladder every 50k years for a billion years.
For example if the fire-control computers aboard nuclear missiles suddenly became self aware and decided that the only way to ensure human suvival is to blow up the humans that are technologically capable of creating them, would you trust them if they presented a solution?