Taking a look at the newest 50 questions with the windows-domain tag, they are all about AD domains with the exception of this onethis one, which is about Samba.
While there surely would be cases where a question only concerns the actual directory service (e.g. something about the schema, an object type or an attribute value) most questions are the much broader case of want-to-get-things-done-with-my-Windows-Server-no-matter-how.
I am not sure about the actual tagging policy at Serverfault (does each and every corner case get an own tag?), but I think a merger would not hurt as the merged tag still would fulfil the general purpose of grouping similar questions with the added benefit of more eyes reading them (active-directory has way more followers).