I understand that you have pretty much already solved your own problem - but just as an alternative, have you considered using Net::Traceroute?

Timeouts would be taken care of for you, and your code could be significantly simplified. Here is a short example script to illustrate, that does basically the same as your get_traceroute sub.

#!/usr/bin/perl -wl
use strict;
use Net::Traceroute;

my $host = shift;

my $trace = get_trace($host,3,30);
print $trace->{_text_accumulator} and exit;

sub get_trace {
    my ($host, $query_timeout, $timeout) = @_;

    my $trace = Net::Traceroute->new(
        host           => $host,
        query_timeout  => $query_timeout,
        timeout        => $timeout,
        );

    return $trace;
}
[download]

Hope this helps,
Darren :)