I don’t want to install gvfs with all its friends just to be able to delete files from within Atom/Electron. However, the environment variable ELECTRON_TRASH can set another trash handler, e.g. trash-cli, which is dependency free.
So I append the variable to my .bashrc and live on as a happy man.
# pacman -S trash-cli --noconfirm > /dev/null
$ echo "export ELECTRON_TRASH=trash-cli" >> ~/.bashrc
Restart Atom and continue to enjoy life