When you rename the main.php file Admin Tools is no longer active. You can of course completely remove the plugin manually by deleting the directory plugins/system/admintools. If you are feeling really paranoid you can also delete the entire component, i.e. the folders administrator/components/com_admintools, components/com_admintools and media/com_admintools. At this point you don't have any trace of Admin Tools on your site.
If the problem persists then it's quite obvious that the problem you have is unrelated to Admin Tools.
I would venture a guess that your problem might have had to do with either caching or a broken / out of sync #__sessions table. I am saying this since you IMPLIED that you were able to get into your back-end, did something and then you could no longer login, all the while the Admin Tools system plugin being disabled.
Finally, I am not sure what is the '"secret" trick in PHPMyAdmin' you are talking about. If you mean disabling the secret URL parameter, let me reiterate that since you have renamed the main.php file the plugin does not load. As a result any kind of Web Application Firewall protection including but not limited to the secret query string parameter and the automatic IP blocking is NOT active.
The only other two things you could have possibly modified on your site with Admin Tools and which will stay behind even if you followed my instructions above are the .htaccess in the root of your site and the .htaccess and .htpasswd files in the administrator directory. Connect to your site by FTP and make sure you've enabled showing hidden files. The remove the .htaccess file from your site's root AND the .htaccess and .htpasswd files (if present) from the "administrator" directory. Finally, create a new .htaccess file in your site's root using the contents from this: https://github.com/joomla/joomla-cms/blob/staging/htaccess.txt (that's the official htaccess.txt shipped with Joomla! itself).
By doing all of the above you have completely undone any possible change you might have ever done to your site with Admin Tools. If you still have a problem after doing that you have a problem unrelated to our software.
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!