I've updated the Navigation-Based Core Data Application Xcode project with the logic from my last post to handle the section problem. As before, unzip and copy the folder to this location, replacing the one that's there:
/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/Project Templates/Application/Navigation-based Application/
I've submitted this to Apple in a bug report, but I don't know if they'll update the official template. They may not want something quite this complex in the template, but until they resolve the underlying problem, I want to make this available. So here it is.