All of the protection rules (WAF and .htaccess Maker) are designed to be dynamic and reversible. It is my creed that no action should leave a permanent mark on your site unless you are explicitly forewarned. The only actions which do modify your site is changing the Super Administrator ID and the database collation. All other actions are reversible, even without access to Admin Tools.
Regarding Joomla!'s self-promotion, it's not half as bad as you describe it. Have you used Windows? You can't get rid of the countless references to Microsoft and the Windows logo sitting right there on your face on the Start menu. Same thing with Apple. Mac OS X puts you the Apple logo on the top left corner of your screen, no matter what. Other CMSs also follow that approach. Try building a site with Drupal, WordPress or any other CMS. Their name is always in the Generator tag and it's not always easy to replace it or turn it off :)
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!