Not sure if this is a kosher way of doing it, but this is the way I've been doing it for quite some time. Also, on a side note I think you've confused what the Qmail queue is.
If you want to remove all messages for a particular user, I simply:
#Remove read messages
rm -rf /home/e-smith/files/users/%username%/Maildir/cur/*
#Remove unread messages
rm -rf /home/e-smith/files/users/%username%/Maildir/new/*
%username% would be the name of the user. If you wanted to remove all messages for all users, you could create a perl script to enumerate the user directories and place that into a variable then execute the above commands replacing %username% with that variable.
Hope this helped,
Nathan