Depending on how time-sensitive your operation is, and its nature, something like this might work:

my $n_secs = 30;  #seconds after which we die.
my $start = time;

## each iteration of this loop is short, but the whole
## thing is long
while ( $some_condition ) {
    die 'We ran too long!' if time-$start >= $n_secs;

    ## do stuff ##
}
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Of course, this will fail miserably if you can't check time regularly; since I don't know what your implementation looks like, I can't say if it will work for you or not. As for putting it in a module:

package RunKiller;

sub new {
   my $self = shift;
   my $obj = { timer => time(), length => shift };

   bless $obj, $self;
   return $self;
}

sub check {
   my $self = shift;
   die 'Ran too long!' if time-($self->{timer}) >= $self->{length};
}

1;
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Called like:

require RunKiller;
my $runtimer = RunKiller->new(30); #30s run length.

while (1) {
   $runtimer->check();
   ## do something ##
}
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