Remember in season 2 when "Ben" stole Henry Gales identity after his death, well what if all this time he had stolen bejamin linuses identity and has been living under that alias. For all we know ben can shape shift, if he can summon a black smoke then he could do that, maybe he had plastic surgery to look more like him, but id doubt ben will live and if he dies then michael emerson has been lying
Also ben says i really hated him meaning his dad may be dead before sayid shot him, maybe bens dad is dead and ben is dead and then michael emerson and someone else managed to look like them and take their place, cuz right now no one knows their dead or harmed