Thanks for putting those two quotes together. I've been dimly aware of not having a good grasp of Anne's rationalisation at the end. But now it looks very much like the "I should have suffered in my conscience" part refers solely to the act of flouting Lady Russell's advice. Even though Anne's decided on long reflection that the advice was bad, she still felt a sense of duty to the adviser.

Anne's hypothetical pangs of conscience seem pretty similar to some of Emma Woodhouse's real discomfort.

Emma ch8, re separating Harriet from Mr Martin, emphasis mine>

She did not repent what she had done; she still thought herself a better judge of such a point of female right and refinement than he could be; but yet she had a sort of habitual respect for his judgment in general, which made her dislike having it so loudly against her; and to have him sitting just opposite to her in angry state, was very disagreeable.