I've mentioned this before - I am not even sure if Rachel is a natural or permanent sub.
She is a loyally married woman who does not get fucked by her husband as he isn't capable.
Susan is a sort of substitute for her non-existent sex-life and the 'pain' is to ease her guilt for feeling frustrated.
She would be feeling terribly guilty about her uncontrollable interest in the MC's cock.
How she behaves once she starts getting orgasms from a man is going to be interesting.
Of course the status quo could be maintained. The MC pleasures her, and she lets Susan punish her to ease her guilt for enjoying proper sex again.
If Uncle persuades her that he is actually pleased the MC is bonking her silly, she may decide she doesn't need Susan quite so much.