The Dark One purposely provoked Rumple into stabbing him in order to free himself from the curse of being the Dark One. That’s why he made the comments about does Rumple really know if Bae is really his son (implying his wife was unfaithful, not that Rumple stole him from someone else). The Dark One knew that would make Rumple mad enough to stab him with the dagger which would then transfer the curse to Rumple. From what I could tell, Rumple seemed pretty horrified when the Dark One changed back into a man and he realized who he had just stabbed. Until that happened, he thought he had stabbed an evil and Dark presence, not necessarily a human being. Remember, Rumple doesn’t consider himself to be a man either since he became the Dark One. I simply had the feeling that Rumple was trying to protect Bae from the truth about his mother. Because if she truely left Rumple because he was coward, then that means she left Bae as well. So to protect Bae from knowing that he was abandoned by his mother he told him that she was dead.