The long-time standard module Symbol to the rescue. Just change undef %Foo::; to delete_package('Foo');.

#! /usr/bin/perl -w
use strict;
use Symbol 'delete_package';

my $s;

print "Creating functions\n";
my $x = TellDestroy->new(sub {print $s}, "variable sub");
*Foo::function = TellDestroy->new(sub {print $s}, "glob sub");

print "Clearing variable\n";
undef $x;

print "Clearing glob\n";
delete_package('Foo');

print "Exiting\n";

package TellDestroy;
use Scalar::Util qw(refaddr);
my %function_name;

sub new {
  my ($class, $self, $name) = @_;
  $function_name{refaddr($self)} = $name;
  bless $self, $class;
}

sub DESTROY {
  my $self = shift;
  my $name = delete $function_name{ refaddr($self) };
  print STDERR "$name is going away\n";
}

__END__
Name "Foo::function" used only once: possible typo at ...
Creating functions
Clearing variable
variable sub is going away
Clearing glob
glob sub is going away
Exiting
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lodin