Does Erring Conscience Bind?

In Too Late the Phalarope the central conflict of the book is that the Lieutenant, a man among men, does not feel a repulsion for black people in the way that his apartheid culture demands he must. He sleeps with a black woman and this leads to the social downfall of his family. And yet, Paton shows us that it is right that he is not repulsed by black people, despite the "Christian South Africans" who cannot see this truth at all.

Huck Finn faces a similar conflict: he knows Jim as a person, but still feels as if he must turn him in for running away from slavery. Twain writes about Finn's internal conflict when he isn't able to turn Jim in:

They went off and I got aboard the raft, feeling bad and low, because I knowed very well I had done wrong, and I see it warn't no use for me to try to learn to do right; a body that don't get started right when he's little ain't got no show -- when the pinch comes there ain't nothing to back him up and keep him to his work, and so he gets beat. Then I thought a minute, and says to myself, hold on; s'pose you'd a done right and give Jim up, would you felt better than what you do now? No, says I, I'd feel bad -- I'd feel just the same way I do now. Well, then, says I, what's the use you learning to do right when it's troublesome to do right and ain't no trouble to do wrong, and the wages is just the same? I was stuck. I couldn't answer that. So I reckoned I wouldn't bother no more about it, but after this always do whichever come handiest at the time.

The irony here is that Huck thinks that he is sinning. He feels that he is a confirmed sinner because of something that the readers know to be a right choice--helping Jim escape. Really, we see that his conscience is divided: he would feel bad if he turned Jim in, and he would feel bad if he didn't. Is he sinning, then? Bonaventure says that he is responsible to change his conscience. But how does one know how to do that? The best that I can think it is possible to do is to educate your conscience within your religious tradition (through seeking councel, reading, etc.). But what is one to do in the case of the Lieutenant, when one has the intimation that one's tradition itself is corrupt? What resources do we have through which to critique our tradition?