This is a really interesting article. LINK I actually embrace the story angle of Section 31, and the challenging whether Gene's vision is sustainable. That said, the writer does have a point, that maybe the new timeline hasn't earned this quite yet.
The writer acknowledges that darker aspects of Starfleet and the Federation have been dealt with outside of DS9 with one whole (rather dismissive) sentence, but then treats that as an exceptional aspect of DS9. I agree that DS9 explored that dark side in greater depth, but it's hardly exclusive to that series (Cartright and the Khitomer conspiracy in particular come to mind as a comparison to Marcus, but there are many more examples) and STiD. The writer just kind of conveniently glosses over the points that don't fit their premise.
Considering DS9 buried heroism and denied the possibility of militancy being a positive force in the last episode, I wonder if the author even thought about the similarity of the series to the reboot. Saying that they were both dark trivialize DS9, which was still very much in the Roddenberry universe, testing idealism rather than ignoring it.
Wrath of Khan worked perfectly as a standalone film, just as Into Darkness does. DS9, a couple of crossover episodes aside, works as a standalone series. All that "earned" stuff is nonsense, IMO. "Space Seed" was optional backstory at best to WoK, just as TNG is to DS9 and the whole lot of Trek is to Abrams' movies.
The use of Section 31 is where the similarities end. Unless...unless the alternate universe of nuTrek is actually the Mirror Universe, and we're seeing the prequels! If nuSpock starts growing a van dyke in nuTrekIII, we'll know!
I only glanced over that article, but Starfleet having darker aspects is hardly unique to DS9. Just look how often we saw renegade Captains or Admirals on TOS, TNG, their movies, and even Voyager. The shows themselves often portray the crews of that particular series' hero ship as noble and virtuous but Starfleet in general has often been rather shady with less than ideal officers achieving high ranks. Hell, often whenever a captain or admiral has gone rogue and the line "impossible, he's a decorated officer" is used, that to me is a red flag that it most certainly is possible. In many ways Starfleet is much like the Time Lords on Doctor Who with how many renegades exist within something supposed to be the most noble and enlightened people in their respective universes.
Using her comparison method; if DS9 served as a counterpoint to all the Trek which came before it then couldn't NuTrek be viewed as a counterpoint to the entire Primeline?