It's not pretty, but it works

my %r;
$r{123}{a}=3;
$r{123}{b}=2;
$r{456}{c}=5;
$r{456}{d}=7;

my %new_r = map {
    my $max_inner;
    for my $inner ( keys %{$r{$_}} ) {
        $max_inner = $inner
            if !defined $max_inner || $r{$_}{$inner} > $r{$_}{$max_inn
+er};
    }
    ( $_ => { $max_inner => $r{$_}{$max_inner} } )
} keys %r;
print Dumper \%new_r;
__END__
$VAR1 = {
          '123' => {
                     'a' => 3
                   },
          '456' => {
                     'd' => 7
                   }
        };
[download]

If there's anything you don't understand, ask!

update: now returns a hash, as per OP's update