The instructions were for a git clone-type installation specifically. If your distribution ships letsencrypt as a package, I would recommend using your package manager to uninstall the client (i.e. apt-get remove --purge letsencrypt for debian-based distributions).
I imagine pacman has something like --purge as well, but I’m not familiar with Arch.
Note that I didn’t attempt to uninstall any of the dependencies the letsencrypt-auto script installs through your package manager, because that depends on your distribution and could easily break things if you’re relying on one of those dependencies somewhere else.