It was fairly predictable, but I'm OK with that -- this is Nick Fury we're talking about. LMDs are part of the whole deal.
I don't think Fury's been an LMD for an extended period; just since "Battle Scars," when he lost the Infinity Formula. It would just be horrible if Fury was an LMD throughout Secret Warriors, and I don't think Marvel has any reason to do that, TBH.
I am not very good with mysteries, so I don't really have too many guesses about what exactly is going on -- I don't think Nick Fury's behind the death of the Watcher, but as I speculated before, I do think he's been running off-the-books assassinations for years.
I doubt that Marvel would make it a rogue LMD behind it all...I think that's a little too simplistic, but it is certainly possible.
At the end of it...I hope Fury survives and becomes the new Watcher. I understand that fanbases should let characters go, from time to time, but Nick Fury...in his own way, he's important to the Marvel Universe. I understand that someone, somewhere, probably thinks it's confusing to have "Samuel L. Jackson" Fury and the original, but who's fault is that? The readers who like the interactions the original Fury has with the entire Marvel Universe shouldn't have to pay a price for something like that.
*Sniff, sniff* "Damn it, Diana...If I'd known they would trade us in for a JT Krul-written Captain Atom and "The Savage Hawkman," I'd have let Superboy-Prime destroy all reality.""Superman flies and is really strong...what the fuck else do you need to know?!"
-- Hitler, expressing his displeasure about DC rebooting and complaints about continuity