"Admitting the Reapers were right all along", thats a funny statement. Choosing Synthesis or Control doesn't mean that we think the cycles were right. Synthesis stops the cycles because the Intelligence's purpose has been fulfiled. I'm not sure what you're trying to say about Control? So what if Shepard becomes the new Reaper master consciousness? It doesn't mean he'll continue the cycles.
You're accepting two things when we agree with the Catalyst: (1) that the organic/synthetic thing is a problem; and (2) either that there is no solution (control) or that a metaphysical blender is the only solution (synthesis).
Choosing the either of the two means that you think the repears were basically right - they just went about it the wrong way without exploring all their options or using the right blender.
This creates a moral problem: you're condoning by implication that where the reapers went wrong is in going to genocide first, not in going to genocide at all. The Shepardlyst takes the genocide machines to enforce galactic wide peace. Ask yourself - how would this thing interfere in the Geth-Quarian war? Extermination short of the point if wipping out either side. Do you think what the Geth did originally wasn't genocide? That's the endgame for the Shepardlyst while it tries to sort out a different solution.
And synthesis is just out and out genocide. It's the planned extermination of two forms of life and culture. Just because it works out pretty awesome doesn't change what it fundamentally means to pull the trigger on it.