Hmm, I'm not quite sure what you're trying to accomplish.
People will sometimes feel guilty when reading a book because they conclude that they shouldn't be reading something like this. Like, "this book is really obscene" or "this book is really racist" or some such, and the reader concludes that he is only enjoying the book because of his own dark nature that his better side decides he doesn't want to encourage. But I think you're saying that that is not what you're looking for.
The other possibility is to present a story in which the reader is lured in to cheering for a character to do something that is immoral or unethical, and then to turn it around and highlight the harm that this character's action does, so the reader is left saying, "Oh, yeah, what was I thinking, why was I hoping the character would do bad thing X? Is it because I would do bad thing X in those circumstances? I really need to examine myself."
Like, the hero is married but one day he meets a younger, prettier woman. The story is presented so that the reader will naturally say, Yeah, go for it man! Your wife is boring and mean and ugly. You should just run off with this woman. It would be so fun and exciting and you deserve it. Then at the end suddenly show it from the point of view of the wife, how she has done nothing wrong and yet she is abandoned and betrayed and how all along the supposed hero has been selfish and shallow. If done right, the reader could be left thinking, "Why did I WANT the hero to abandon his loving and devoted wife for cheap sex? Would I betray people I claim to love and care about for such shallow reasons?"
Similar things could be done with a story about stealing, anger and violence, racism, etc.
All that said, unless your point is to write a harsh story about some social issue, I'd be very reluctant to write a story that tries to make the reader feel guilty. People don't generally like to be made to feel guilty, so this is probably not a recipe for a popular book.