I gotta call "fan-wank" here. It's great fun to see so many not-so-mainstream references to TOS in this issue. That being said, however, I'll bet less than 1% of what's in these comics makes it into the movie.
Look at the last "Countdown" series, leading up to the 2009 movie. We were treated to all of the TNG cast -- Picard, Worf, Geordi, so on -- we were told the Narada was Borg technology, etc... etc... etc...
But when the film hit the big screen, the ONLY thing that carried over from the comics was that Spock and Nero had fallen into a wormhole, after the destruction of Romulus.
So, come May, I'm guessing the only likely elements of this miniseries to end up in the movie are the debate about the Prime Directive, maybe Robert April (if so, it's Peter Weller), and something we won't see until the fourth issue.
A Bajoran Mudd is nothing more than wishful thinking and a distraction. It'll never see the light of day when the movie is released, because of the fact it's too obscure and intricate. And you can take that to the bank!