So the only logical conclusion is that the Catalyst is lying about this option, trying to trick you in some way.
I do not see said logic, considering this option is closest to its own benefit both objectively from what we know and from its own report. It would stand to reason that if it was trying to trick you, it would do so away from the outcomes it does not desire.
Control puts too much power in the hands of one individual, and if there is anything that history has taught us, it's that absolute power corrupts absolutely, even a paragon Shepard with the best intentions.
You mean like an agent for one of the most powerful government entities in the galaxy, granted authority that supersedes the law in Council space? 
Destroy brings the galaxy back to its natural state, chaos. Let things evolve as they are going to evolve. That's the way it was before the Reapers, and that's the way it should be. Survival of the fittest.
Uhh, that really is not desirable at all. Virtually all the comforts of modern life today -- from modern-medicine to HVAC -- is a subversion of the state-of-nature and survival-of-the-fittest (the latter, by the way, is not even the most important component to evolution), and the human condition generally improves by further subverting nature's hold/limitations on intelligent life.
If synthetics end up wiping out organic life, so be it. Organic life had their chance and was selected against. And who's to say that organic life is preferable anyway. Sentient beings are sentient beings. Let it be decided naturally, instead of dictated by the Reapers.
Well, letting the natural course decide things is what led us there in the first place (to the Reapers rising to the position of dictating).
If letting nature just take its course is a good idea, even if it leads to AI coming out on top, why bother with fighting the Reapers?