Hi jabramson623,
Unfortunately there is no way to Automate this process. There are few Applications which doesn't get updates using RUM. They are Acrobat, Lightroom, Muse and CC Desktop app.
Could you please let me know whether your Users download the apps on there own or do you manage the same for them. If you manage then you can disable the CC Desktop app while creating the Package so they don't get any update prompt for CC Desktop App.
Please let me know if it answers your query.
Regards,
Abhijit