Install a clean Mavericks and then use TimeMachine makes it unclean again?
It depends on your definition of 'dirty' — indeed, restoring from Time Machine will restore many preferences, but won't restore any system files, as they will come from your fresh OS X install.



If you want the cleanest possible OS, manually copying the files you need will be the best option — even though it's time consuming, you'll only get what you need.

The OS itself will remain 'clean' if you restore from Time Machine since the files will be kept from the OS X install and won't be restored from Time Machine.