In an Active/Standby Master configuration, you definitely want both controllers running the same version of code, because in a failover scenario, you don't want your APs to have to upgrade/downgrade code.
I would handle this in the following way:
1. Pre-load controllers with new version of code.
2. Shutdown VRRP on active-master to failover APs to backup
3. Reboot active-master to load new code version
4. Make sure pre-emption is NOT checked and bring VRRP back up on active-master
5. Shutdown VRRP on backup-master to failover APs back to active and they will upgrade their code
6. Reboot backup-master to load new code version
7. Bring VRRP back up on backup-master and test failover again.
Not sure if this is what you would be suited for, but I think this would help to minimize down time.
Thanks.