Then today I noticed this Apple Support document that details iWeb 1.1's ability to handle more than one website/database file. Now, you can create multiple database files and work on them separately. In fact, you can keep these files anywhere you want to; not just in your Application Support folder.
Check out the Apple Support document for details on how to create a second iWeb database and how to handle working with multiple sites. There are a couple of minor gotcha's, but overall, this should be good news for anyone who wants to use iWeb to create and manage multiple, completely separate websites (publishing to non-.Mac locations, of course).