Sometimes you need to restrict users to use work items or make it obsolete. We can't delete a work item type from the process template, so we must find other ways. I didn't find a good solution for that issue. (There is an article from MS, how to make a work item obsolete, but I needed other solution. read here: http://msdn2.microsoft.com/en-us/library/ms184761.aspx)
You can do that by editing work item type definition for the type and setting permissions on the first transition:
<TRANSITION from="" to="Opened" for="YOUR DOMAIN\USER OR GROUP" >
That way, only authorized users can open work item of this type.