Rename VM in VMware Fusion via command line
Well, there is no rename, it is a multi-step process, which involves renaming a bunch of entries inside the vmx file, using vmware-vdiskmanager to rename to vmdk and in general doing a bunch of potentially problematic actions if you don't know what you are doing.

You could probably write a quick Perl script to do all that using this guide.

Another option would be to clone it and delete the original, but it is resource intensive and does way too much work for what it is worth. The code below is untested:

vmrun -T fusion stop "/Volumes/vms/old/old.vmx"
vmrun -T fusion clone "/Volumes/vms/old/old.vmx" "/Volumes/vms/new/new.vmx" full --cloneName=new
vmrun -T fusion deleteVM "/Volumes/vms/old/old.vmx"
vmrun -T fusion start "/Volumes/vms/new/new.vmx"