I haven't read your post - shame on me - but I do know there's a BIND::Conf_Parser. More specifically, there's a $self->handle_zone( $name, $class, $type, \%options )
Could it be that this is what you want?
Thanks much for the CPAN link, but I'm simply trying to avoid installing it on a machine just for the sake of deleting an entry. I might just use it though :)