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.