Did they even have a story locked in for the film eighteen months ago when the comic was written?
AFAIK, the basic story of the sequel film had already been decided before IDW got the go ahead to do an ongoing series of comics based on the first movie. Orci tells them which episodes they can remake, and he approves each one. He is seeding easter eggs into each issue. We won't realise bits of trivia are easter eggs (eg Dr Dehner once had a relationship with McCoy) and which are red herrings until the new movie comes out.
And would they let a comic read by, maybe 10,000 people, stop them from doing a story for a $185 million dollar movie?
They wouldn't, but the comics had 77 other adventures
to choose from, and yet Orci approved them using "Where No Man..." first up, thus reintroducing Mitchell and Kelso (and killing them off), and remaking the encounter with the Great Barrier. Orci is on record as wanting
the comics (and
the new computer game) to tie-in to the new movie, generate positive word-of-mouth and create one, big, new tapestry, which already includes the popular "Countdown", "Nero" and "Spock Reflections" mini-series from IDW.
Orci and the Bad Robot team also asked Pocket Books to shelve four tie-in original novels set in the same time period. No official reason has been given, but it's easier to vet twelve or so comic two-parters over several years than four novels that were going to come out in a short timeframe.
To satisfy that 10,000 comic buyers, who are spreading that positive word of mouth, it's highly unlikely Orci would approve a story that duplicates "Where No Man".
Now if Cumberbatch turns up and Kirk says something like, "Gary, my old Academy friend - it's you! But how? We all thought you were dead?"
maaaaaybe it would work, because the unseen, offscreen, mysterious past event he is referring to isn't needed for this brand new story about a resurrected friend who suddenly has enough superstrength to battle a Vulcan on the rim of a volcano.
But the film is not
going to be a color-by-numbers remake of "Where No Man..."
Honestly, I've had that Cumberbatch is playing Finnegan in the back of my mind for a while now.
Yep. Or a shape-changing Captain Garth. I can even imagine Garth taking on Gary's appearance, and Kirk knowing its a fake because "the real Gary died months ago".