If you need to kill a guest VM via the command line, use the vmware-cmd command.
"vmware-cmd /<path to VM directory>/server.vmx stop"
"vmware-cmd -l" will get you your virtual machines names and config file locations
If that does not work you can take more drastic measures and kill the VM process itself.
ps -ef | grep <virtualmachinename>
kill -9 <pid>