Are we sure this is a directory limitation? Or is it regional?
My ward's online directory has displayed preferred names for quite some time. My ward just merged with another, and you can actually delineate quite accurately who was in my ward and who was in the other ward before the merge by looking at who has full names and who has preferred names showing in the directory. I think it has more to do with what is set at the preferred name in MLS.
Have you looked in MLS? I seem to remember that the default preferred name was the same as the full name. I went through my ward's records and changed all of the preferred names in order to get the online directory to appear with the preferred names. Is it possible that your directory is displaying the "preferred name," but that the "preferred name" is no different than the "full name?"