There is no working way of actually removing CRM users from the database; I think one reason is that it would cause all the records previously owned by a now deleted user having no owner at all (the same goes for the createdby and modifiedby fields), which would put the database in an illegal state.
The official way of removing a user from the CRM system is deactivating the systemuser
record. This does not sever the connection to the AD user, however, but I think deactivated users should not cause problems when reimporting the organization; I'm not sure of that, though.
You could theoretically delete the systemuser
records from the database using SQL, but that's highly unadvisable.
Changes in the AD users are actually causing various issues with MSCRM quite often; a larger customer even had us develop a solution for automatically synchronizing their CRM users with the state of the AD because managing that manually proved to be too much work in a large environment with a few hundred users.