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.