All permissions and user details are inherited from your VCS (GitHub or Bitbucket). To remove a user from the CircleCI account, they must first be removed from the organization on your VCS.
We are not able at this time to remove users from your organization's active user list mid-billing cycle. At the end of each billing period users who are are not actively building will drop off from your list of active users. This is to ensure that anyone who is not pushing to CircleCI is not counted as an active user.