First of all, make sure you can remotely manage the hyper-v server from another machine. Once you have this set up, you can use the MMC and add the Certificates snap-in for the Hyper-v server object. You can then import the CA certificate to the trusted root certificates store.
Oddly enough, I came here in my search for this exact same answer, and out of all the different blogs, forums, etc... discussing it, none have mentioned this method. It was while doing the searching that it dawned on me that you can use MMC to access a remote system's certificate stores.