on CentOS: 

$ sudo yum remove git

Next, you can completely remove the /opt/letsencrypt directory (the directory that you downloaded the LetsEncrypt repository to).

$ sudo rm -rf /opt/letsencrypt

If you actually generated a Certificate using the instructions in the guide, then you’ll also want to remove this following directory:
(If you already installed Certbot, this will also remove any certificates generated by that tool, and it could possibly break your Nginx/Apache configurations)

rm -rf /etc/letsencrypt

(I know you’ve already done this, but just for the sake of it…)
If you added the Cron entry to your cron table, then you’ll also need to remove that line. You can open the cron table with this command:

$ sudo crontab -e

Then, you’ll just want to remove the following line:

0 0 1 * * /opt/letsencrypt/letsencrypt-auto renew

Source: https://www.linode.com/community/questions/17003/how-do-i-remove-a-custom-letsencrypt-installation