If Henry finds out Bae’s his dad, making Rumple his Grandpa, then he may start having ideas about one big happy family get together. Hook’s revenge quest against Rumple would hurt that, which in turn would hurt Henry. Emma wouldn’t allow that.
Emma’s and Hook’s relationship is doomed to failure. She wouldn’t want him to take revenge against Rumple, and he would resent her if he was forced to give up his revenge.