Unfortunately, the Bitnami-bundled Apache distribution is not integrated with Let's Encrypt. In fact, executing that option might install Apache the DEB package on your system, over your current Bitnami Apache.
In order to disable it, try the following:
sudo /etc/init.d/apache2 stop
Next, start your Bitnami Apache:
sudo INSTALLDIR/ctlscript.sh restart apache
In order to install and generate certificates with Let's Encrypt, we recommend you follow this guide: https://docs.bitnami.com/installer/components/apache/#how-to-install-the-certbot-client-for-the-lets-encrypt-certificate-authority
I hope it helps!