I think mail-journaling applies toe every email that enters or leaves your Domino-server, so I guess it will journal emails sent to external addresses too. (Makes sense, since it is used to journal email for legal purposes and compliance).
For your non-domino situation: I would recommend setting up a Linux box with an smtp-server (PostFix or whatever), and configure it to log all email traffic (date/time, from, to, and subject). This way, it does not require any modifications to your application. The logs will also give you exact information why your mail has not been delivered too. If a user claims they did not receive your email, but the logs indicate that the mail was successfully delivered to their mail-server, it's no longer your problem ;-)
It's not hard to set up actually. I have a linux-box myself with PostFix installed, and I use webmin (a web-based tool to admin your linux box) to check the logs.