Exactly. Trek is about, "When faced with Hard Choices, you should still Do the Right Thing."
Actual line from the last Section 31 episode of Deep Space 9:
"Doctor, you've been a beacon of light to me. You're living proof that ideology is a poor substitute for kindness and decency – and that, at the end of the day, it's our actions and not our beliefs that define who we are, what we are."
Sloan might as well have turned to the camera and said "Always do the right thing, even if it's hard."
It all comes down to a refusal to let stories end.
The original Suicide Squad comics were good because anyone in them could die (it was even believable Amanda Waller could die since there were others who could take over and it looked like she might sacrifice her life in the last comics), the original Section 31 episodes were good because it was never clear if Section 31 was officially sanctioned or a conspiracy.
And both were tied directly into the storylines they were part of and addressed what was going on in the time periods they were written in (directly in Suicide Squad since it's set in the modern day, metaphorically in Star Trek since it's the future).
Keeping the stories going past that required removing that ambiguity (DC isn't going to kill off cash cow characters permanently and Star Trek revealed Section 31 WAS official and basically Federation secret agents), butchering previous characterizations (original Amanda Waller was at worst an antihero, she would never do the vile actions her modern versions do and as I previously mentioned she realized the Suicide Squad had to end and Section 31 being official makes the Federation look like hypocrites), and just having the stories be generic stories as opposed to offering commentary.
It's not fans blindly repeating "The old stuff was better," it's a legitimate case of incredible storytelling being stripped of everything that made it meaningful in favor of generic cash-ins.
Actually this has inspired me, I got the complete original Suicide Squad comics as a birthday present, I'm going to do a review of them.