I don't know what you mean. http://www.turkishdictionary.net/?word=judge "yargiç" means "judge. Why would you "always" add the possessive suffix? Here the possessive suffix shows that it is a possessor. "yargiçin" means "judge's" or "of the judge" or "of a judge" or "the judge's" or "a judge's" So, perhaps you were not aware that "the judge's secretary" = "the secretary of the judge".
Not a native speaker, but from what I've learned thus far, "Your judge is his/her secretary," could be conveyed with
Yargıcın onun sekreteridir.
Manisa Turkish has a really good page on possessor/possessed relationships, which is what is required in such a sentence. You can link to it here:
Hope that helps.