you would have to add the VM into your ESXi inventory, but you can use VMware vCenter Converter Standalone 5.0 which encrypts the data. Albeit while encryption is enabled, which it is by default, the process make take sometime.
The VM image would be in our inventory. My end-goal is to be able to offload an image to local storage (i.e. new vm deployment to different sites or offline storage of image gold disks for change management, etc.). I don't think we can use Converter 5, since it's not approved for DoD use yet. We're using 4.1 Update 2. Do you know if Converter 4.1 can encrypt?
the encryption of the data is new in Converter 5.0.