I have posted the same question in the Github Project Repository and this is the complete answer: https://github.com/atom/atom/issues/2195#issuecomment-42917489
The commands to execute are:
sudo rm /usr/local/bin/atom
sudo rm /usr/local/bin/apm
rm -rf ~/atom
rm -rf ~/.atom
rm -rf ~/.config/Atom-Shell
sudo rm -rf /usr/local/share/atom/