When a user is created in Bitbucket's Internal Directory, there is no way to deactivate the user apart from removing its Global permissions in order to free up its license.
This problem doesn't exist when the user is stored in an external directory (LDAP, JIRA or Crowd) which provide option to disable the user.
JIRA has long implemented such option and Bitbucket Server administrators would benefit from it as well in the same format:
Note that removing a user's Global permissions will do free up his license. This won't remove, on the other hand, any other permissions (i.e. Project, Repositories, Branches) for that user.