Frankly I'm surprised it took this long to notice partial hashing as a problem, and to exploit it on a large scale. Anyone giving serious thought to file integrity would notice right away, as soon as they run Kazaa for the first time 3 years ago, that there is no way to fully hash a 20gb share in just a few seconds. Ironically, the biggest original complaint against eDonkey was that it took a long time to add files to a share. Duh, no shit.
The only way to fix the situation now is for Sharman Networks to rewrite the FastTrack protocol (and it really would be a major overhaul) and have everyone rehash all their files. Might as well switch to Overnet now
And full hashing doesn't even take THAT long. On my lowly P3 1GHz, eMule takes about 30 seconds to hash a 700MB movie file, and of course these are cached so you only do it once. Even if you remove a file from your share and re-add it later, the hash is remembered. If you keep your files on a remote file server, this will be a bit of an issue, but again, you only gotta do it once.