For what it's worth I've had the 4gb since they were released and the first thing I did when I got mine was take the shell off my old Elite's 120gb hard drive and stick it into my 4gb. It plays Halo Reach just fine. I haven't been banned. The drives are plug and play and there is no update or flash required for installing it. I really doubt they check to see if your hard drive is in the console it was bought with, if they banned people for using hard drives that didn't come specifically with their system then why would they give the option to purchase stand alone certified drives in store? The drives, whether purchased separately or taken out of a shell from another system, are still certified Microsoft drives.
If people are still paranoid about something happening then why not just ask Xbox Support? They will probably say something like "yeah, it's possible but not recommended because the shell on the new drives is like it is to hold the drive secure in the console and we can't be held accountable if something messes up because you have your drive just hanging in there without a shell".