Re: Can I get a certificate WITHOUT running their software?
Yes you can, well sort of. You need to run the software, but you can prevent it from doing anything to your config. https://github.com/letsencrypt/letsencrypt
A bit down the page it says you should use ./letsencrypt-auto certonly --standalone [...]
That will seemingly not install anything. Only fetches the cert for you to do with as you please, from my understanding. (I wouldn't let some random tool meddle with my config either, but there'd always be backups and "diff" to trace the exact changes it made; plus it's open source, so probably not that hard to work out what it does)