El Capitan updates killed my Mac, again

This is the 3rd time this has happened in 6 months. I just accidentally accepted App store El Capitan updates and again it has left my iMac in a completely unusable state. I am able to login and see all files in folder, however folder is the only application that I can run. If I attempt to run anything else, including App Store/Safari/Terminal, I get an error "You can't open the application "[App name]" because it may be damaged or incomplete.

It previously happened about 6 months ago when I updated my iMac and Macbook Pro simultaneously, mysteriously occurring on both. I tried a chat session with Apple but really the only recommendation is to reformat and restore from time machine. Yes, I have everything backed up but this is starting to become a real pain now. I have apps installed that will require me to have the vendor reset licensing (recording software) which causes a 1-2 week downtime for me.

Can anyone help? In the GUI my Applications folder shows completely empty, but if I browse via Terminal in Recovery mode I am able to see all the applications. Maybe my user account is no longer in admin?