The most fitting answer is: Shelby is mistaken in thinking Haley is a man with conscience.
This is ironic because Shelby, while expressing concern for Tom's character and integrity, is also willing to hand him over to Haley, who is depicted as morally questionable. Shelby’s remarks about Haley's conscience highlight the contrast between her view of Tom and her decision to allow him to be sold, revealing a lack of moral integrity on her part as well.