An additional important piece of information for new players:
If you accidentally kill someone, you MUST restart from a save. Simply killing Snake and replaying the area will still register a kill. (Same goes for Alerts.)
If you do want to restart an area for any reason (and you haven't killed anyone), just give Snake the lethal pill. Don't be tempted to throw a bunch of grenades, as you may accidentally kill an enemy soldier in the process.
(I learned all this the hard way!)