In the comic version of "The Galileo Seven," Spock never has his worldview — i.e. that command decisions can be arrived at through logic — challenged. Worse is that Uhura's rescue robs Spock's act of desperation, which is the climax of his character arc in the episode.
I was a little annoyed by that, too. But after some thought, I also see this different ending as a completely logical outcome. Unlike in the original timeline, this Boma had probably served under Spock during the brief period when he was Captain of the Enterprise. Everyone probably would be a little less inclined to argue with him given his history. Plus, for some reason, he decided to try and take the dead body with them up in the shuttle vice unceremoniously dumpin it. These was a big point on contention between Boma and Spock in the original version that didn't happen in this version.
And as for Uhura rescuing them vice Spock getting to do his moment of desperation. This actually makes sense. In this timeline, with Uhura and Spock as lovers, they probably have some small telepathic link that would allow her to find him on the planet even though sensors didn't work. This wasn't the case in the original timeline.
I also found it interesting in the comic how Kirk was able to pull out some obscure Starfleet regulation to get the High Commissioner off his back. Kirk in the original timeline didn't do this. What are the writers trying to say there about nuKirk versus the original timeline? Maybe nuKirk sees that he's a little out of his element, promoted so fast, and is taking extra time to study things like regs and historical precident so he doesn't make stupid mistakes. Or maybe the writers just felt it was a more realistic outcome than the original episode, where they just coincidentally saved the day just in the kick of time without Kirk's actions causing that save.