Prevent Atom quitting on Cmd-Q
System Preferences → Keyboard → Shortcuts tabs → App Shortcuts. Use + button to add new shortcut and enter exactly what "Quit Atom" menu item says in atom app. I use cmd + escape for Safari, VSCode and Xcode where I accidentally press Q instead of tab, w, 1, 2, 3 etc. and it's been great so far.  I've been using it for ~3 months now.

Both global and application defined shortcuts work.  Unique menu item is the key. 

I am on Mojave.