Merlin’s warning didn’t make any sense. He told Emma not to pull the sword from the stone. Forget the fact that Emma didn’t even do it, the sword was pulled in present day storybrooke in 506, meaning that anything that happened before wasn’t the consequences that Merlin was talking about, so Hook turning into a dark one would have happened regardless if Emma pulled the sword. Everything that happened after she pulled the sword from the stone, didn’t happen because she did it. Nothing was a consequence of that act. Hook would have still wanted revenge, he would have still opened the gate to the Underworld, which didn’t even need the sword in order to do it, only Rumple’s blood. In addition, they needed the sword to get rid of the darkness, even if it had caused bad things, it would have still been inevitable because it was necessary.
In my opinion, Neal’s warning will be nothing more than dramatic effect. From what I understood, his warning was generic “Don’t do it, bad things will happen” yeah, no kidding.
"All your questions are pointless"