Track-it 11.4? The importer can be configured to accomplish this, specifically to remove the user license. The user record stays as it is associated with assets, tickets, etc.
See the online help article at http://documents.bmc.com/products/trackit/247/Help/EN/desktop/Administrator/Directory_Importer/Directory_Importer_Overview.htm.
Which refers to the KB article at http://support.numarasoftware.com/support/articles.asp?how=%20AND%20&mode=detail&kcriteria=6478&ID=6617
Which says open the TrackIt.Core.DirectoryImporter.xml and find the setting 'deleteUsersNotFoundInAd' from false to true
this XML is located in %Program Files%\BMC Software\Track-It!\Track-It! Services\ConfigurationData\
If you actually want to completely delete a user from the system, beware of the associations in all the different tables. Its safer to just leave the record in there.