In the strictest sense, Jane Eyre is all about morality – in fact, it’s close to being didactic (it's as if Brontë was trying to teach her readers about ethics). Characters seem to have an innate sense of right and wrong, and it isn’t difficult to tell what decision to make in an ethical crisis. It is, however, extremely difficult for these characters to make ethical choices in a world where morality and passion seem to be mutually exclusive. Characters must choose between being right and being happy. Luckily, in the end, circumstances will conspire to get all the ethical obstacles out of the way so that we can have the happy ending we’ve been craving.
Jane’s decision to abandon Rochester when she discovers that Bertha is living creates a separation between her and the reader; while Jane chooses ethics over passion, the reader is caught up in the romantic plot, rooting for love to triumph over everything, even morality.
The true "moral lesson" for Jane is not that it would be unethical for her to be Rochester’s mistress, but that it would be unethical for her to be St. John Rivers’ wife.