How do I erase partitions on a drive that's been protected with FileVault 2?
You can use diskutil cs list to show the core storage view of things.

Once you have the logical volume UUID for the disk in question, you can use diskutil cs deleteVolume to clean up the reserved space that was allocated to the encrypted data and filesystems. That would allow you to surgically remove the core storage.

You could also unmount the filesystems and nuke/pave the drive:

diskutil unmountDisk disk6
diskutil partitionDisk disk6 GPT ExFAT Files 16g