I have a similar mindset, but I don't think its a matter of sticking the genie back in the bottle. I think its a matter of establishing what are the limits of Section 31 and what they are not able to do.
For starters, we really don't have mention of them in TNG and really don't see them come back in to the picture until the Dominion War. And I think that is really telling in terms of their overall influence, and how it is diminished since TOS era. And that, for me, is the positive.
No, I don't like Section 31, but I also don't believe they are the dark glue that holds the Federation together. I think that is their moral justification for their existence, but that doesn't make it accurate or right.
My view on them is relatively simple-they are a holdover from prior to United Earth and the founding of the Federation that kept trying to manipulate and control events to support their own power and ends. Over time, they became less influential as the Federation became more powerful, and gave less and less credence to their methods, allowing Starfleet to act more in the Federation's interests (like Kirk in "The Enterprise Incident, or Picard in "Chain of Command.").
It's only when a threat is so dire that we see them try to assert power. That doesn't make the Federation less optimistic. It just makes it very human.
At least, to me.
They are willing to do what no one else will do to ensure that the majority of the population can continue being blissfully unaware of just how close to the edge the Federation has come in the past.
They dont need recognition or medals like some glory hounds and are content to remain in the shadows.
I especially like that they only act if absolutely necessary and when all other avenues have failed, it shows they understand and practice restraint at all times, otherwise they would be running the show, that is probably why the Federation/Starfleet tolerates them.
I really did like the Sloan character in DS9, he came across as a very genuine individual who meant what he said, not at all surprised that they asked Georgiou to join, I bet the staff roster for S31 is very colourful indeed.
I would totally join as an Intergalactic Man of Mystery.
If you think about it the Dominion war was ended via blackmail, Bashir/Odo said to the founders that they can either surrender and receive the antidote or die out, something that Sloan would have approved of if he had lived, understandable that a part of him didnt want to take that chance and tried to stop Bashir from getting the cure.
While I do think the Alpha Quadrant could have won in the end due to the Dominion being cut off from reinforcements the death toll would have been unbelievable, same goes for the Klingon War in Discovery.
This is why I loved the plot lines of the Dominion war and S31, it was entirely believable right down to Garaks manipulation of the Romulans and Sisko hating it but knowing it had to be so, to be honest if the Romulans had found out about the trick they would probably have gone along with it anyway in admiration.
Its easy to sit in an armchair when at peace and all is well throwing stones, quite another when your whole way of life is threatened, the Federation/Starfleet know this and that is why S31 is tolerated/tacitly approved of.