Corporate Intranet: Best Practice

Keep the top-level site blank, use publishing features, make the welcome page point to a lower-level site (not the top level site).

Remember, if your site managers and content owners have permission to modify content types on the top level site, especially core content types, then maybe WSS and MOSS isn't your thing after all.

Once that core content type is changed (like renaming the 'title' field in the 'item' content type), then you are screwed. Nuke from orbit and start all over, and yes, start ALL over is the only way out of this one, folks...