The only time Courier rewrites headers is when a message is sent by the sendmail command, and the -bs option is not specified. Messages received by SMTP (which includes sendmail's -bs option) are left untouched.

The sendmail man page lists various environment variables which the sendmail command uses to set the From: header. Most system-generated messages, from cron, etc???, are sent by running the sendmail command, so this may work for you. You'll need to figure out how to make arrangements so that the sendmail command, when invoked by various system processes, has the right environment variables set.