The anti-soy issue I believe has more to do with GM than the soy itself... same with corn, cotton, canola, etc.
If you read the anti-soy propaganda GMO is not the major issue. The claims refer to the aluminum they claim is in soy, the goitrogenic effect, the phytoestrogens and the phytic acid mainly. But the same people making the claims apparently do not have a clue about the chemistry behind these things and the benefits of some of them.