We received and answered this question via email last week. For everyone else's benefit, I'm pasting the reply we sent via email below.
There is currently no built-in option to detect if a user is logged into the system when deploying a package. To achieve this you will have to create a custom script. The script needs to include a user logon detection and perform the install only if no user is logged on. We can however not provide support for custom scripts or deployment packages. Adding a built-in user detecting process for the deployment feature is added to the wishlist but we cannot yet provide a release date for it.