An old confucian saying, 'What has been done, cannot be undone' (as written in the little book down at the local courthouse. hee, hee, hee....)
Seriously, I am afraid that you are stuck...well, I mean your wife is stuck. As far as I know it cannot be changed again...ever. When my wife decided (or we, actually) decided to have her name changed in order to make sure one mistake wouldn't lead to another (which it did anyway...har, har, har....) they told us...and I very clearly recall the words...if you do this, you can never go back to the Japanese family name; is that ok.
So, unless the law has changed somewhere (and I seriously doubt that, the legal systems looks good in moss, they seem to think) your wife has no choice but to use your family name or...maybe it's possible...remarry.