This can be turned off by going to System Preferences > Accounts > Login Items. Once the Login Items opens simply uncheck the application and this will shut the process off the next time you reboot the system.
Now that you have shut it off then you can just remove it so that it doesn’t come up the next time you reboot by highlighting it and then clicking on the (-) remove option.
You can manually turn the ColorMunki Photo Tray back on at any time by going to Login Items then clicking on the add option (+) and navigating to:
Library > Application Support > ColorMunki Photo > Tools > ColorMunki Photo Tray.app.
This has been reported to our development team and being worked on for a future update of the software.