This story has some elements of urban myth in it - see http://www.snopes.com/critters/crusader/stuffedtoys.asp
As they point out its not only stuffed toys that are treated with anti fungals/bacterials - fillings of duvets/doonas/quilts/comforters/ pillows/cushions/pet beds are all potentially treated with the same chemicals.
Also there is no details that if you wash toy/quilt whether the chemical is removed/reduced.
I would also be very surprised if there were any standards imposed on what is deemed appropriate or safe for pet toys - there seems to be little or no regulation as to what can be fed/added to pet food around the world.
That is not to say that there are very good manufacturers of pet food/toys who take the research upon themselves. However if I went along to my local craft store and bought a commercially available filling, how would I know whether it had been treated or not?