How to sign a CSR from OpenSSL using a Microsoft 2012 R2 CA?

I have generated a CSR on a Linux computer using OpenSSL - no problems there. However, I have 2 specific challenges:

1. I need to use a Certificate Template that is on my MS Windows 2012 R2 CA
2. I need to sign this CSR with my MS Windows 2012 R2 CA and somehow get it back to the Linux box

As you know, Windows 2008 R2 was the last CA system that supported the web enrollment page concept, where you could simply paste in a Base64 encoded CSR and have the system spit you out a signed Certificate to download.

Anyone know how to do this? I've tried taking the CSR and copying it to the CA and then using certreq.exe, but this always generates an error because it wants to suck up the local CA system's hostname and cram it into the Certificate... Help?