There should be some way of marking a directory as being pruned without having to edit /etc/updatedb.conf. One method would be for the existence of a certain dot-file within the directory (like .MLOCATE_PURGE) to signal that the directory is to be purged. Another method would be to set a particular extended file attribute on directories to be purged.
/etc/updatedb.conf
.MLOCATE_PURGE
Possible configuration options:
/home