All WUs that are sent out are sent out 3-4 times anyway, so it shouldn't matter too much if you just go ahead and delete them. However, if you are still going to be running Seti for a bit, go into the web admin of SetiQueue, and go to Settings, and change the settings, and change "Download new Work Units" to "Disabled". Then, when clients connect, it will still give them new WUs and take their results, but won't download any new Work Units. Continue this until you have drained the Queue, then it should be OK
Otherwise, just uninstall/delete the directory, and point your clients somewhere else, and it will also be fine
Garry