I ran across this paper which documents a very low tech method of reducing exposure to fumonisin exposure from corn. The down side of this approach is that it is labor intensive and ~4% of the corn has to be thrown away. I'll point out that one of the benefits of expressing a Cry gene in the ear is that there are less ear worms and as a result, less fumonisin producing fungi.
There are many ways of dealing with any problem, each with costs and benefits. What is appropriate here?