That's all good and dandy, but even tough your module looks useful (and generic), I can't say I like the resulting interface — i.e. the use statement. I'd rather see something like this:

use strict;
package Foo;
use isa qw(Bar);
sub new { bless {},shift }
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The module isa.pm can actually quite short:

# file isa.pm
package isa;

sub import {
    my $pkg = shift;
    my $caller = caller;
    no strict 'vars';
    push @{"$caller\::ISA"}, @_;
}

42;
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Et voilà:

foo is a Bar

Of course, with base doing the same and more, I don't know if there's much need for this here module.