There's the small issue of the body of Locke being in the matal case they dragged around the island. There's also the fact that Ben strangled Locke and hung him up from a rafter.
But since its possible for smokie to make 'replicas' then its possible the body in the coffin is actually just a 'fake' body and that the alive Locke has just been possessed by MIB. I like that thought as I am very interested to see how the Locke we all know and love will return in series six. I can't believe he's now just going to play an evil dude.