So please do not be "captain-save-a-unix-n00b"
This is what made me think you were saying you knew Unix.
If root login is enabled, then someone can potentially hack into your box -- all they need is a password to be god on your machine. If root is not an option, the most they can do is what your user account can do. If root login is disabled, I really don't see how any hacker can gain those privileges. But one of the major reasons that I know of for disabling root login is security -- not trashing system files. I, of course, am no expert on security.
My personal computer's security is pretty guaranteed. How do I know this? I connect via dial-up connection. I can pretty much guarantee that no one in their right mind will try to use my computer for a DOS attack.

And since I keep no sensitive data on my computer (all personal info, like financial stuff, is kept on offline media -- so they'd have to break into my house to get the info, and if that's the case I'm screwed anyway), I'm not too worried about people poking through my HD. Heck, even if they did find something that they wanted (probably software) it'd take them at least 24 hours to upload it somewhere else.

And I don't leave my connection on that long...
Hmm -- can't really point you to a thread, since I'm not on any Unix fora currently. Maybe a search on google might turn up some articles.
Since I am a new Mac user (last experience was with System 6!), I'm not sure about the System Folder thing. Won't the OS prevent you from moving the system files?? I know that it won't let you do stoopid stuff like partition your boot drive, so I assumed that it would have the same protection for the System Folder.