Thanks! So with this being fixed, setting up Let's Encrypt is actually even more easy than in the HowTo. All you have to do is:
1. Get letsencrypt-auto:
git clone https://github.com/letsencrypt/letsencrypt
cd letsencrypt
2. Run letsencrypt-auto. It installs all dependencies (at least on Debian):
./letsencrypt-auto --server https://acme-v01.api.letsencrypt.org/directory --help
3. Get certs. Use the webroot of Hiawatha to authenticate the desired domains. The letsencrypt-auto script puts some files in the /.well-known/ subdirectory. These files are downloaded by the Let's Enrypt server to verify you are the domain holder:
./letsencrypt-auto certonly -a webroot --webroot-path /srv/www/example.com/ -d example.com -d www.example.com --server https://acme-v01.api.letsencrypt.org/directory --agree-dev-preview
4. If this succeeds you can copy the certs to the hiawatha config directory (hiawatha need's a specific certificate format), add the file to hiawatha's config and restart the hiawatha:
cat /etc/letsencrypt/live/example.com/privkey.pem /etc/letsencrypt/live/example.com/cert.pem /etc/letsencrypt/live/example.com/chain.pem > /etc/hiawatha/tls/example.com.pem
chmod 400 /etc/hiawatha/tls/example.com.pem
/etc/init.d/hiawatha restart