I'd look for a custom DNS challenge provider plugin which delegates the task of creating DNS records to another machine which holds the actual token.
> Get certificates for remote servers - The tokens used to provide validation of domain ownership, and the certificates themselves can be automatically copied to remote servers (via ssh, sftp or ftp for tokens). The script doesn't need to run on the server itself. This can be useful if you don't have access to run such scripts on the server itself, e.g. if it's a shared server.
* https://github.com/srvrco/getssl
It's written in Bash, so dependencies aren't too heavy.