As LanX had guessed, non-deferred signals can do what you want. It's not that pretty, but it works.

#!/usr/bin/perl
use strict;
use warnings;
$|++;
my $s = 0;

use POSIX qw(SIGALRM);
POSIX::sigaction(SIGALRM, POSIX::SigAction->new( sub { warn "skipping 
+$s (took too long)\n"; die } )) || die "Error setting SIGALRM handler
+: $!\n";

my $str = 'ffvadsvefwdvewrfvt4vketwrhjkbveqwkjhfkghjlfghjkufghjkfhjkfj
+kgfghfkhjfkhjgfhjgfhgfhkgfhkgfhkgfhkgfkhjgfkjgfkghjfkhjgfhjgfkhjgfhjk
+fk' x 40960;
$str .= 'hjkbklklhbjklercvqewrqereqrfqeerv;;;jnrveervnlknrvlerlvnerlnv
+elrvnervlkenvlervojubnertvffff;kn;kff;kn;fk;k;;kmnff;knmf;nff;mnkf;;k
+;;' x 40960;
my $str2 = $str x 8;
my $str3 = 'furrfu';

my $re = qr/(f((\w?)(\w*?))?)+/;

print time . "\n\n";

for ( $str, $str2, $str3 ) {
    $s++;
    my $res;
    alarm 2;
    eval {
        $res = $_ =~ s/$re/ ^_^ /g;
    };
    print "$s made $res\n" unless $@;
}

print  "\n" . time . "\n";
exit;
[download]

This puts out something similar to the following, given the system is slow enough to take more than a second on that second string but not on the first (or third -- gosh, let's hope not!).

1401392795

1 made 1310721
skipping 2 (took too long)
3 made 2

1401392798
[download]

This is perl 5, version 16, subversion 2 (v5.16.2) built for darwin-th
+read-multi-2level
(with 3 registered patches, see perl -V for more detail)
[download]

Update: Per davido's advice in the thread, I'll point out that the above is tested but not thoroughly so. One might hope that the die() and ending the eval would be enough unrolling of state that no segfaults or other wonkiness would happen when the regular expression engine is interrupted and reinvoked. If not, the forking model does make a lot of sense. One might also put code for handling one regex at a time into a separate script and hand off to that with something like IPC::Open3 which will handle parts of the child management and inter-process communication for you.

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