Is restoring a Time Machine backup on a clean install of OS X Mavericks still a 'clean' install?
If you reinstall 10.9, don’t choose "Restore from Time Machine Backup". Make a simple install after you reformatted your drive with Disk Utility.

After the install, the setup process will start and you can choose if you want to restore from Time Machine. I would recommend you to deselect the System to restore, just your home directory and your applications. So you will just restore your data (docs, music, pics), your applications settings (~/Library) and the application bundles from /Application.

This the closest you can get to a "clean" install, without manually migrating your data and setup again every single app.