Soy...what should I do?

For nearly 6 weeks I've been working with Take Shape for Life and using Medifast products in an effort to lose weight.  I have needed to get quite a few pounds of for a long, long time and finally had enough.  I've tried over and over to control things on my own, but decided I needed a temporary plan that would allow me to not have to think about what I was going to eat all day.  TSFL/MF seemed to fit that package perfectly.  I have an aquaintance that has lost over 80lbs through this plan and that put me over decision's edge.

Before I started it I had a lot of misgivings.  My most prominent concern was the fact the MF products are primarily powdered meals.  Everything from shakes, to soup, to scrambled eggs...it all starts out in powdered form aka NOT anywhere near the whole organic foods I've come to believe should be the only thing we should consume.  My second concern was the amount of soy contained in the products.  Soy is not fertility's friend (remember it took us 8 years to have Elliana).  I've known that for years.  Extra weight, however, isn't doing my fertility any favors either.

6 weeks into the program I am very pleased with the results.  I've lost nearly 20lbs and for the most part have felt really good.  I still have a long journey ahead, but getting back to a healthy weight actually seems attainable for the first time in years.  This all added up to me pushing my concerns about fake food and "the evils of soy" as far back in my brain as possible...until I read this article.

Now everything I fear has been conjured back up.  What if I'm causing more damage to my hormone function?  How is all of this soy isolate affecting my thyroid?  How permanent are the affects of soy?  What's more damaging, 80lbs of extra weight or 6 months of a heavily soy based diet?  Is there a way I can get the same results on my own with an all natural diet? Would I be able to have that much self control? 

My heart is a bit heavy.  I want to be free of all of this weight that I put on due to hormone imbalance and heartbreak.  I also want to get my body in the best condition possible to have another baby.  I want to do both without hindering either pursuit.

God made our bodies with intricate wisdom.  He created food to perfectly fuel us and balance us.  He designed us to be productive and reproductive.  I'm praying that He will show me what to do.  I need clear practical answers.