That's the thing... they still use fertilizers and pesticides. They're just "natural", but copper sulfate, pyrethrins, and rotenone don't strike me as all that natural. They, too, could have effects that take decades to come together. Indeed, some "natural" pesticides, like arsenic and nicotine, are already banned.
My problem here is largely with the industrializing of the "organic" label. The things that you're really hoping for -- crop rotation, co-planting, mulching, no-till, etc -- don't really scale well. The organic farms look a lot like conventional farms, enormous monocultures. The names on the labels are just different.
I'm presenting the negative case here, just to point out that I'm really not certain. I'm a big supporter of what JI Rodale was doing when he popularized the term "organic", but that's not what you get in the grocery store. I have hopes that the grocery store is in fact ultimately a little better for the planet, but I wish I could be more certain.