setting a script time limit won't help (the browser will time out..)
do you need confirmation that the job is done or that it has started properly??
I would have thought that exec'ing the shell script with an " &" after it would have kept it running in the bg after php execution finishes. But if you need completion feedback, you might want to use an email notifier or have a php page that checks for completion refresh every minute or so.
Cheers,
Tim