I don't really see the connection to Christian marriage in master/mistress (or, er, I see it, but its not what typically comes to mind).
I just remember learning in grade school about when to use Mr., Miss, and Mrs - and similar nouns to address persons in other languages such as French and German. While the guy is called [X] regardless of his marital status, women get two noun/adjective/appellation/thingies, usually with the marital status/age heavily implied in their appropriate usage (Frauline, Frau; Madam, Mademoiselle). Miss is for unmarried women, Mrs. is for married women. Though, I guess now you can use Ms. instead (when I was taught that crap, "Ms." was for divorced women).
And "mistress" is such a dorky-sounding word.
The connection to slavery was purposeful, as Cyrodils have been enslaved, and in my mind much of the system for formal speech originates from these times.
If they resented slavery, wouldn't they try to avoid using terms that were linked to slavery (e.g. Master)? I mean, they were and are all against the whole slavery thing. So, why would they address each other as "Master Rufinius" or whatever if "master" is the term they had to call their oppressive Ayleid owners?