The Starchild's logic is faulty. If an individual studying either public speaking, English, or even the philosophy of logic were to break down the Starchild's argument for its very existence they would come to a consensus that it's grasping at straws, and illogical. You have a deus ex machina (the crucible) and a diabolus ex machina (the catalyst) that the entire ending is revolving around, which is a huge no-no. Another big issue with the ending was that it pulled WAY too far back in way too little time. The entire scope very suddenly and sharply broadened with no gradual in-between to guide us into the fact that: omg, god-child, what? There is this root conflict that's suggested between organics and synthetics since Mass Effect 1. Saren talks A LOT about that; he also hints at the fact the Reapers are the solution. The Starchild talks about what they do as the "solution." So there's some sort of a connection, but it is so... so stretched. The solution is to the problem of synthetic creations always rebelling against their organic creators.
With "synthesis" essentially with everyone the same, with organics being partly synthetic, and synthetics being partly organics, the Reapers are no longer needed--but they still exist. Gigantic hole. What's to stop the Starchild from suddenly thinking that maybe this new hybrid race is going to create something dangerous?
Here's where the logic breaks down: While the Starchild seems convinced that it's doing organics a favor, preserving them in horrendous fashion... actually... I have something to say about that. From Mass Effect 2, we've come to understand that the way the Reapers harvest beings is by... turning them into some sort of... slurry. Yum. If that's how they preserve the minds/essences of each being into a new cuttlefish, then how could the Reapers still function in a machine-like fashion, if they're filled with nothing but minds whose last thoughts were utter fear, pain, despair, and overwhelming hopelessness? That's just... my thing. So good job Starchild, you're really operating on the three laws of robotics aren't ya?
Anyway, so the logic of the Starchild breaks down like this: Its objective is to rescue organics from themselves, before they create synthetics who will, as the Starchild so firmly believes, always rise up in dissent. The issue, is that the Reapers themselves, as synthetics, are the ones perpetuating the cycle. They are the ones carrying out what the Starchild believes they are protecting the organics from. The Reapers, in reality, are not actually taking preemptive measures, but rather are the perpetrators of that which their very existence was supposed to protect the galaxy from.
Did your head hurt? Mine did. That's the reality of what we have as the foundation for THE ENTIRE ending, which then is supposed to make us believe is the foundation for the story throughout the ENTIRE SERIES.