I think you really have to completly uninstal all your SMS 1.2 clients with a tool in the login script (I've one if need).
Then uninstal the logon servers, backup some important datas (smsls.bat, queries, packages definitions, custom mif files, static groups) in order to implement these settings into the new SMS 2.0 site.
Then disconnect the SMS 1.2 site server.