This may sound like a bit of a technicality at first, but bear with me for a minute.
John Locke is not dead. Yes, we can see from the flash forwards that we've been shown that Locke will definitely die in at some point in the future, in the show's "present," (I know that's quite a relative term at this point, but I'm thinking of the present as all the characters' on-island present.) Now, according to Lostpedia (http://lostpedia.wikia.com/wiki/Timeline:Post-Return) and the general consensus of the Lost fandom, the Ajira flight departed some time in January of 2008, and Locke, Illana, Caesar, etc. were transported in time back to 2007. So if Locke dies in 2008, and the present is 2007, then he is not dead.
While this may sound like a technicality (I agree, he obviously looks dead in The Incident), we know that time is everything on this show, or, as Eloise Hawking would have it, time is the essence.
I'm not precisely sure about how to interpret this fact, but it seems like one of 2 scenarios could be possible for season 6:
1) A Not-Yet-Dead-Locke, wherever he is now, will somehow come bounding onto the scene with Richard, Ben, and the Lockleganger. This would mean that there would actually be 3 Lockes: Dead-Locke-in-the-Crate, Not-Yet-Dead-Locke, and the Lockleganger.
2) Locke's dead corpse will be resurrected because it's not supposed to have died yet. Presumably one would have to ask why this didn't happen immediately upon reaching the island and being transported back in time, but I'm thinking that maybe something has to happen first to bring it about. And for some reason, I think it might involve Jack being some kind of constant, and he'll have to believe that Locke is not dead.
Anywho, I'm not so great at predicting how things will play out. The writers are much better at this than I. My main point is simply to say that regardless of anything else that can be said, it's an undeniable fact that Locke has not died yet. He is presently alive.