I now want to delete the VMFS volume from the 3.5 cluster and shutdown it's hosts, while keeping the volume in tact on the 5.0 cluster. I am concerned that, once i right click on one of the host in the 3.5 cluster and delete the vmfs volume, all of the virtual machines on this cluster will be deleted as well.
Don't delete the volume. You are correct that this would at least attempt to destroy the VMFS partition. As was stated earlier, since no workloads are running on these 3.5 hosts, I would just power them off.