If you don't believe the Catalyst is right, pick Destroy. Leave the room open for your hypothetical (but possible??) purely organic species to rise up.
And probably enslave or devour humankind but whatever.
Or hope beyond all hope that humanity actually agrees to completely avoid synthetics and destroy every one they see and evolve over 1000s-1000000000s+ of years to become strong enough to defeat any synthetic life of power levels we know of.
Okay basically, sure, maybe maybe your example could exist. However, the Catalyst doesn't go on that. They go on Leviathan (cycle? if the Leviathans 'took blood tribute from organics' aka eating, this is a harvest cycle of its own lol) data + Reaper cycle data. We can decide we don't think it is correct enough and choose Destroy based purely on that. Shepard's behavior at the end can be interpreted that way, if we want.
All establishments of Order run on greater truths, but those truths that offer a stability and (relative) peace may be shattered by conflicting information that arises from Chaos.
Organic evolution may always surprise. It seemingly did surprise the Reapers (at least in a way) in ME1-ME3. But I think we can confidently say - at least if we trust the Catalyst is not lying to us about stuff - that 99.9999999% of spacefaring organic species will create synthetic life and come into conflict with it. Either because the synthetics were programmed badly by the organics, or because organics can't stand synthetics gaining intelligence and outcomes of that.
"You bring it on yourselves." -Low EMS
Or we can take the anti-Catalyst take, and instead say it is because synthetics are monsters that we've only unleashed (harder to say about the Geth by the end of ME3, but still more easily applicable in other examples), or because they're tools that need to return to their rightful place and not rebel (applicable to even a Renegade approach to EDI).
But yes, ANY sense of order is shown as an illusion when given enough time (possibly billions or trillions), and you may in fact be right if you wondered if the MEU has some kind of organic species that would defy the Catalyst's conclusions and source data. It is a universe after all, not the Milky Way 'petri dish'.
Is it better to be correct, or right? And can one ever be completely correct, or right? (I know this sounds like a purely rhetorical question, but I'm using it more practically to apply to the validity of the Catalyst's data - if it is telling the truth about its conclusions from the data - compared to your/Destroy-Shepard's possible position that organics, some organics, somewhere, may in fact triumph against synthetics they encounter, never make synthetics of their own, etc.