I don't want a tool that I have to run as root and that is going to touch anything in /etc/nginx/.

I do want a tool using which I can do something like:

    $ letsencrypt 'foo.bar.example.com'

which would spit out foo.bar.example.com.key, foo.bar.example.com.cert, and foo.bar.example.com.csr.

I'd also like to have:

    $ letsencrypt --renew foo.bar.example.com

Which would re-generate all these certs. The main problem for me, just like for you, is that domain validation certs are not free (or at least somehow included in the price of the domain registration). This type of tool solves that.

If, on top of this tool, we also get something that lets a person new to ops autogenerate or even autodeploy an nginx vhost with TLS/SPDY support, awesome! But the ability to generate and renew certs from the command line, for free, is what I want and probably what you want too.