The potential health risks of eating a large amount of soy seem to be related to natural compounds in the soy plant, not a side effect of genetic modification, non-organic farming techniques, or over-processing.
I think it is generally safer and healthier to eat whole foods, but even natural foods can contain some levels of chemicals that can affect the human body in harmful ways and that's one reason that eating a varied diet is so important.
In the case of soy, there are phytoestrogens which are good mimics for human hormones and can have noticeable effects. I eat more soy around PMS time and it helps reduce my symptoms. The phytoestrogens produced by soy plants are a defense mechanism and help prevent overgrazing (birth control for herbivores).
Ever since I heard about the study that linked tofu consumption with low brain weight, I've been careful to limit my soy consumption. But I still eat it as part of a varied diet.
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