Moderator: Thread moved to the vSphere Upgrade & Install area.
You really don't have other options. It was a poor decision in the first place to co-locate DNS–a core, critical piece of infrastructure–with vCenter Server. You'll have to rectify that somehow, someway prior to moving forward. The best way you probably do that is deploy a dedicated DNS server (which is what should have happened to begin with) and make it a replica of the existing one. You could then re-point DNS on the co-vCenter/DNS box to this external DNS server, and use that DNS server for the upgrade/migrate wizard of the vCSA.
Regardless of what version you have and wanna upgrade to what release, co-existence of critical services such as DNS server and vCenter server like your deployment is not a good structure and you should separate them anyway. As a temporary solution to your situation is implementing an additional DNS server include zone and all required records (A, PTR, ...) to use during vCenter reboot.
However Windows-based vCenter server is not supported any more in recent release (version 7) and you should upgrade it to an Appliance-based (VCSA) soon.Please mark my comment as the Correct Answer if this solution resolved your problem