Non-organic organisms would still require the biosphere to self-propagate on earth. Currently they need organic and inorganic matter to operate. Assuming they stayed purely mechanical constructs, they would need the byproducts of the earth to maintain themselves, and there are limits to those byproducts and the rate at which they can be produced, not to mention the rest of the biosphere that supports their production.
If they somehow evolved past mechanical constructs towards more chemical/biological machines, or some sort of electro-mechanical construct that wasn't constrained by a physical/machine form, they would, as far as i'm aware, still require the biosphere to propagate or at the very least interact with us.
Even if they did want to fuel a spacefaring civilization (why???), why would they cannibalize the earth when they can already travel to planets, moons, asteroids, etc which have more of the components they actually need to function? Unlimited access to solar power, more heavy metals, and aren't restricted to the limitations and detriments of our biosphere (oxidation, gravity, ionosphere, electrically conductive material falling on you all the time, etc). On top of all that, there'd be these damn adaptable irrational homicidal monkeys that fear anything that could threaten them, and many things that don't. It would behoove them to get the hell away from Earth as fast as possible.
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Anyway, all this assumes that somehow they could adapt faster than humans. I know of no plausible timeframe that anyone can yet estimate when this would happen. Kurzweil says 2045, but this makes no sense when you look at our actual progress over the past 50 years.
We still travel on Boeing 747s fueled by million-year-old decomposed plant juice. The richest nation in the world has one of the least advanced train systems in the world that only covers a fraction of the country. And one of the leading causes of death are the heavy speeding metal boxes we manually pilot through free space that are insanely less efficient than any other modern mode of transportation, purely because we like cars the most.
Predictions of technological advancement over 15 years in the future don't work because human progress is not based on capability. Much like your fear of a fate you can't be sure could even happen, our future is not based on what could happen, but what we make happen - our will.
Just as it is "possible" for us to birth a matricidal organism, it's just as possible for us to willingly never create such an organism. And since we imagine this supposed event would end in our own destruction, and we are [in general] on the side of self-preservation, it's not likely we would willingly pursue this event. It would be more likely if the idea never occurred to us.
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Great civilizations have existed several times with advanced science, then fell, and took several millennia just for others to get back to where they had been. In terms of what is actually a threat to ours today, climate change and an unstable political/socioeconomic climate actually will kill us in a few decades if left unchecked. I suggest we focus on the immediate threats before we sweat the theoretical and philosophical ones.