Going from an installation profile to vanilla Drupal
Once a Drupal site is installed, it doesn't really matter which installation profile you used. The only difference is that it's possible to use modules and themes that are located in the profiles folder. So in that sense you are running vanilla Drupal.

If you want to disable the possibility to use the modules from the profile you need to, once you have added the modules to sites/all, set the installation profile to "standard". The easiest way to that is to use drush:

$ drush vset install_profile standard