The correct way to prevent users from utilizing certain types (including built-in types) in Documentum is usually to configure the client. For most clients this is done using display configuration through the DD (Data Dictionary) mechanism.
However, for My Documentum Desktop this seems to be somewhat different. I have not used it myself, but take a look at the My Documentum Desktop Installation and Configuration Guide 6.7.2, page 25 -- Object type filters preference set:
This sets the root object type that generates the list of object types from which users can select in the ingest dialog box. This also hides specific object types from display in MDD.
On page 56 -- Define settings for an object type (Windows):
Default_Document_Object_Type=dm_document
I guess the former configuration setting will help you in hiding dm_document, and the latter could assist you in making a default type choice for clients.