Because once they strike him down he will becoming even more powerful.
Ya know, considering all the people he's essentially gathered to be on the island, there might be some merit to your comment. Perhaps his power lies in those he can win to his cause and his death makes them stronger.
the other guy found his loophole. so did jacob. he prepared for this. by his death, the things he set in motion will pick up speed to finally end his opponent. i'm guessing whatever they've tried over the long years have always ended on a draw. this time they both went beyond what they normally did to try and end it. time will tell who's plan was better. either way, they knew this time it would be the end for them.