What you are looking for is an encrypted file system, but unfortunately no such animal exists for darwin/OS X.
Surly though you don't need the entire disk secured, right? I mean is it really that bad if someone gets their hands on your /System directory (sure sure, they didn't pay for a license, but that's an Apple problem).
Of course it's perfectly reasonable to want your documents secure, and I think the best solution for that would be to make an encrypted disk image.
Mount the disk image when you log in, use it like a regular disk, then unmount it when your done.