Contact Emirates and ask them to split the PNR.
That will allow one passenger to be upgraded. Whether the other person who is not upgraded is happy with that - who knows? Maybe you will earn enough further miles before the travel to upgrade the other person - but that also depends on upgrade availability.
Three of us have a single booking from DXB-MAD later this year. We have split the PNR into 3 single ones. Mrs bsd and Miss bsd have been upgraded, then availability disappeared. - and I am waiting to see if it reappears for myself.
One potential complication we experienced on another split PNR trip in the past is that it can mess up chauffeur drive - if you provide details for all the party then more than one car can be provided; if you don't then maybe only one car is provided and you have to convince someone that a largish car is needed for more passengers.