Use a deployment framework like Phing to manage deployment to the webservers and get rid of the cron job. Basically, a release on the production system should not happen automatically, but only after you are certain the current build is not broken. And it should not have a dependency on the dev system.
Since Phing uses XML and PHP to configure and control the deployment process, you can version control the process. This is an added benefit, as you can then keep the deployment connected to specific builds of your application.
To prevent the production website from being affected by the deployment process, consider uploading a new build into a separate directory and then just symlink to it. If anything goes wrong, you can easily symlink to a previous version.
Also consider using a CI server.
