I, too am somewhat confused on the seemingly sudden anti-soy movement. I've read some of the links provided and am still somewhat baffled. In all honesty "watchdog" groups will pop up for ANYTHING and often, medical facts and statistics can be bent to support any angle given. Let's not forget how eggs were at one time touted as the world's perfect food and we were encouraged to eat tons of them. Then in the 90's they found links to cholesterol and heart health issues involving eggs and they were consequently vilified beyond belief. They were the worst thing you could eat. Then more studies showed that eggs are indeed good for you and that the earlier studies were incorrect. I mean come-on. I think so much of one thing or the other is just hype.
I garden organically, do try to purchase organic foods when it is feasible in my budget, and I do feed my animals what is healthy for them. I don't have a problem paying more for healthier food. That said, I also have no problem buying food for either myself or my animals that comes from a major producer that may or may not include healthy ingredients. I am as much a proponent of initiatives that will save the earth and promote overall better living for all her living things, but sometimes you just have to go with what is within your means. Someone will always be allergic to something, watchdogs and governments will always find some food to vilify over another (ever think that maybe, just maybe, soy is being vilified so that more money is poured towards other protein sources???), and the world will still go on.
I say if it makes you comfortable then do it. If it works for your budget, then great. Just don't try to make others who may or may not be able to afford one lifestyle over another feel guilty for not taking a similar route.