It might be easier (better?) to just dump the alarm completely, and use select(). That will take care of any safe signals issue, and allows you a bit more control as well

Something like this:

use strict;
use warnings;
use IO::Select;

my $timeout = 20;
my $read_set = new IO::Select();
my $pid;
my $starttime = time();

my $pid = open my $fh, "-|", $command or die $!;
$read_set->add($fh);

while (time() - starttime < $timeout) {
  my ($rh_set) = IO::Select->select($read_set, undef, undef, 1);

  if (defined $rh_set) {
    # note: use sysread() instead of <> to be really safe
    if ($_ = <$fh>) {
      push @array, $_;
      print "+";
    } else {
       # eof
       last;
    }
  } else {
    # nothing received for a second
    print ".";
  }
}

kill 9, $pid;
close $fh;

if (time() - starttime >= $timeout) {
  print "Timed out\n";
}
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Update:Use time() instead of localtime()
Update 2:Fixed open() line