At the moment if you want a user to not count towards the licensing you have to delete that user. The problem with that is you lose the ability to search by that user for comments etc.

We should allow you to deactivate users so they cannot use the application and do not count towards the user total.

UPDATE: when having both FishEye and Crucible licences, there is an option presented to enable Crucible access for individual users, see https://confluence.atlassian.com/display/FISHEYE/Deleting+or+deactivating+a+user. But when having only Crucible licence, there is no way to deactivate the user, the only option is to delete the user.