Is there a setting to prevent drupal from timing out during long operations?
There is (obviously ;)) no setting to make Drupal faster, so you're only chance is to allow it to run longer.
You will only be able to change these settings if you are running your own server. If so, then see http://drupal.org/node/207036 and http://www.php.net/manual/en/info.configuration.php#ini.max-execution-time.
You could also ask your hoster nicely to increase these settings for you, but that might not happen as these settings are usually setfor good reasons (On shared hosting servers are usually tons of users, so hosters want to prevent that one of those users is taking up too many ressources from others..)
Views data export uses batch api to build your export in chunks short enough to be processed properly. And you can safely leave it in cron to generate your data at night, if you need daily updates.
