Do you have more than one site defined in IIS or have you changed or deleted the default website?
When executing the command referenced you have to provide the numeric site reference so that the paramter in the IIS metabase is modified for the specific site within IIS ... so, ifyou have more than one site, you would have to do this for each site.
From here ...
http://windowsitpro.com/article/articleid/42426/q-how-can-i-control-access-to-the-iisadmpwd-virtual-directory.html adsutil.vbs set w3svc/1/PasswordChangeFlag
s 2 would disable the password changing option for the default site, assuming the default site is the default one created when IIS was installed, this is the only site that will have the number 1 (referenced by w3svc//PasswordChangeFlags )
Once you disable this for all of the sites then I would expect that the directory will not come back once deleted.