Reworking the Employees / Contacts modules to incorporate user management in the same place would be a big project.There is, however, a shortcut that would make user management easier.
In both Employees and Contacts modules you could have an option under the "Actions" button called "Invite Employee as User" or "Invite to Supplier Portal" or "Invite to Customer Portal". This button would be only visible to users with access to "Settings".
Clicking the button would open up a pre-populated pop up with the right fields "First Name", "Last Name", "Email", "Role", "Solution", and obviously "Contact Association". This could be similar to the pop up we have for adding related records.
This would simplify the process of adding new employees & users to the system a lot. All you would have to do is add a new contact, and when you save the new contact, you could invite them directly to the system.