"Inter Arma Enim Silent Leges" is classic Latin for "In the face of Arms, The Law is silent." (The translation quoted in the episode is less effective) -- In other words, The Law is powerless by itself. It needs someone and some way to be enforced, and this leads to humans -- and another classic Latin quote, "Quis Custodiet Ipsos Custodes?" ("Who will watch The Guardians?").
In reality, any society requires occasional "black ops", something inherently anathema to the ideal of the Federation, but still required, occasionally, for survival. They can even sometimes be justified in terms of the tradeoffs -- as in "In the Pale Moonlight", if the death or betrayal of one individual can save thousands, is it not the appropriate choice? Ideally, no -- but what about the real world?
This is true even of The Federation. It is not a pure ideal, but a real society, and thus is dependent, entirely, upon the quality of those who supervise it... and they are constrained, inevitably, by their surroundings. Sometimes they must do things they might abhor and revile, but which are needful to survive or even produce a substantially better outcome.
In this episode, we see another case of a Federation Black Op, this one aimed at weakening the Romulans as their primary rival after the Dominion War is over (and, apparently, the Federation now feels confident this will happen in the Alpha Quadrant's favor).
In the end, like Dr. Brashir, you are left with an uneasy recognition that the above is true -- that some people must be allowed, though not encouraged, to act outside the law, so that most can exist inside the law with safety and security.
That the society depends on the overall good ones and not the occasional bad ones... but that it does still need the bad ones, too. As the Oriental symbol goes, a spot of bad in the good.
And, finally, that the ones doing bad may not be evil in themselves, as we begin to see is true of Sloan just as it was of Sisko in "In the Pale Moonlight".
You don't have to like Section 31, but it is needful that something like it exist, even in the Federation mileau.