The nuke sunk the island, and Oceanic 815 never crashed.. so that Sayid, who turned out to be the reason Ben ended up with the Others before Dharma evacuated.. never was there to make that happen.. Which is why we see him and his dad in RL.
About Smokey.. Why was he previously referred to as a security system? What is the loophole that allowed him to kill Jacob and permanently assume Locke's form? Why did Locke have to die for any of that to happen?