[jackalope]

My concern is that your reach is too far. Asking domain administrators to trust your software to manipulate private keys (and server configurations) is as troubling as asking end users to click past security warnings. The whole purpose of the CSR is to obtain the signed certificate without putting the private key at risk. This decoupling isolates the challenge of identity verification in a reasonable place (nobody is saying it's easy). With your client, you're essentially telling people you accept checks or credit cards, but only if they show you their gold. It sets a bad precedent.

I do want your certs for free! But I also want/need to trust you and know that you're following best practices, not just with me but with everyone.

[schoen]

Oh, our software does NOT send the private key to the CA. Never never never never. The point of having it manage the keys is not to give us access to them, it's to be convenient for the end-user, on the end-user's own system, under the end-user's control.

You can tell because our software is open source, written in Python.

https://github.com/letsencrypt/lets-encrypt-preview

We expect the users to get this software from their operating system repos, like from the Debian package repository -- the very same place they get their Apache or Nginx packages. We are not asking people to get the software directly from us, or to use it without being able to read it and check that it's safe and does what they want.

Edit: And if you want to implement your own client, we encourage you to do that -- the more clients the merrier!

[jackalope]

I'd still be more comfortable if the process never went anywhere near the private key (and I'm concerned that a proprietary competitor or look-alike would prey on naive users by leveraging your example). But I also applaud your effort and transparency. I admit I trust openssl to manage my own keys and certificates, and there is definitely room in this space for improvement and alternative approaches. But it does sadden me that we risk making administrators as trusting and ignorant of the underlying principles as end users already are today.