The result of a measurment will depend on how it is done, and the method should relate to the way is is going to be used. If the secondary is to be grounded, the measurement should be done that way. If the transformer includes a faraday shield, the common mode will be nil and hard to measure. I have not had to do this measurement, but I would tie the two primary wires together and drive them relative to ground with a signal generator, measure the signal at the secondary terminals and call the common mode rejection the ratio: sec/pri volts or dB.