You could use open with a pipe in order to get the PID of the child process, and kill it if it doesn't finish in time. Something like this:

#!/usr/bin/perl

my $pid = open my $fh, "your_command ... |" or die $!;

eval {
    local $SIG{ALRM} = sub { die "alarm\n" };
    alarm 600;
    # ... optionally read any output from the subprocess
    # while (<$fh>) { ... }
    close $fh;   # waits for child
    alarm 0;
};
if ($@ eq "alarm\n") {  # timed out
    kill 9, $pid;
}
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Note that if the shell script itself is running further child processes (not that unlikely...), they would not necessarily be killed, too (depends on the behavior/setup of the shell). In that case you'd have to create a process group and kill the entire group in case of timeout. See Re^2: Killing children's of children for sample code.