if everything else fails, you can use a forking open call (see open docs on perlfunc):

#!/usr/bin/perl

use warnings;
use strict;
use Carp;

my $pid = open my $pipe, '-|';
defined $pid or croak "unable to fork";
if ($pid==0) {
    # child process
    print "SCORE=134";
    # my  $aln2 = $factory->align($seq_array_ref);
    exit(0);
}
else {
    # parent process
    my $score;
    while(<$pipe>) {
    if (/SCORE=(\d+)/) {
        $score=$1;
        last;
    }
    }
    print "score=$score\n";
}
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be aware that forking can cause problems if you have open connections to databases or some other resources.

also, $aln2 will only have a value assigned on the child process.