How to force a process to be started by another process

I have an AutoUpdater application that launches another application. Is there anyway to force that second application to ONLY run if it was started by the AutoUpdater?

The problem is, some end-users will create a shortcut to the main app file on their desktop. This becomes a problem because it's supposed to check for updates to the app before it launches, and they don't receive our updates.

One thought I had was to create an IPC channel via WCF and issue a very simple command from the AutoUpdater to the other application. If the other app doesn't receive that command within 2 or 3 seconds it would close itself.

This seems like more code/overhead than what should be needed though. Is there an easier way?

Thanks!