Create a new user in LDAP, not wherever Drupal normally creates it
You will never be able to use Drupal's core user module without using the database's user table (and many others), without seriously modifying core Drupal. 

It sounds like the only reason you want Drupal to not use it's own user + roles + permissions management (and all of the other contributed Drupal modules that depend on the user module) is so that if a user updates some data in LDAP it's also updated in Drupal. If this is the case, find a method for synchronizing your LDAP user info with Drupal's user info.

You can use the hook_user_ functions in Drupal to perform whatever actions you want to happen when a user account is created, updated, etc., in Drupal. For example, if a new user account is created in the Drupal user registration form you'd be performing whatever logic you need (via PHP, or potentially something else) to insert a new record into your LDAP server.