We have no idea what the state of play will be by the end of season 3, or even half way through season 3. The story may very well progress in such a way that Hook is still a vital part of it. Given the huge fan following the character has, I’d be surprised if they wrote him out of the show at any point in the foreseeable future. There are really only 2 people who know what Hook’s longterm story is going to involve, and that’s Adam and Eddy. All the rest of us can do at this point is guess.