Sorry, I must have misread your OP, I thought you were going into Task Manager and killing the vmware-vmx process and this has the potential to and can and will corrupt the virtual hard disk, not necessarily every time. As far as force stopping with the red button yes this only effects the Guest OS not the virtual hard disk.
As to closing the VMware Workstation GUI if you have more then one VM running then this is not really an option although for VM's that have VMware Tools installed the VM should be properly shutdown by that action although again if you have more then one running I wouldn't do it.
To protect the Guest OS and Guest OS Filesystem on the VM instead of abruptly stopping it with the red button you can use vmrun to issue a shutdown or reboot command or another option is ssh into the VM and issue a shutdown or reboot command. Or use RDC/VNC to connect to the Guest OS and issue a shutdown or reboot command.