I may be misunderstanding you, but I think you just want:

delete @hash{keys %end};
[download]

Here's a simple program that demonstrates it:

#!/usr/bin/perl

use strict;
use warnings;

my %hash = (one => 1, two => 2, three => 3);
my %end  = (two => 2);

delete @hash{keys %end};

print "$_ => $hash{$_}\n" for keys %hash;
[download]

By the way, I've taken my specification from your post where you say "delete the keys in %hash if they exist in %end", rather than your code which seems to do the opposite.