Use alarm within your script to schedule a signal, and have your $SIG{ALRM} handler clean up and exit gracefully.

$SIG{ALRM} = sub { exit; };

alarm 60 * 60 * 2;
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Another option is to have your script write a pid file out someplace:

open(F, ">$wherever/myscript.pid") or warn "myscript.pid: $!\n";
print F "$$\n";
close(F);

$SIG{TERM} = sub { exit; };

END {
   unlink "$wherever/myscript.pid";
}
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And then script something like this in cron:

[ -r $wherever/myscript.pid ] && kill `cat $wherever/myscript.pid`
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