In System Settings > Keyboard Shortcuts > App Shortcuts, add the shortcut: app Safari, name "Quit Safari", command-option-Q. This will leave command-Q doing nothing, yet still allow you to quit. Repeat for other apps.
Nah, I installed karabiner and set up command+q to require a three-second holddown to activate.
That's a lot of work to do it per app! And remember to do for every new app