So far I measured CMRR by first obtaining the open loop gain and exporting the wave, and then doing the same with the AC source in common mode, but this adds the need for additional software, and make the process difficult automatize.
I don't think there's any easy way, since the two test circuits are different (basically with the AC source connected as common or differential input), but I wondered if there is any HSPICE trick to make it work.