Going off your description alone, it sounds like the VMware hosts have networked storage (NFS or iSCSI) which when the switch stack reboots, they lose their connectivity to the datastores and therefore the VM's crash.
If that is the case, you will definitely need to change your design.
You could:
- Separate the switch stack into two separate switches. This will give higher availability for VM's during Meraki firmware upgrades
- Use a separate set of switches for the iSCSI/NFS storage connection. This has the advantage of physically separating the storage traffic from general VM traffic. However although the VM's will now stay up and not crash during an upgrade of the core Meraki switch stack, they will still lose Network connectivity.