From In the Pale Moonlight:
SISKO: That Vreenak obtained the rod on Soukara and that the Dominion killed him to prevent him from returning to Romulus with it.
GARAK: Precisely. And the more the Dominion protests their innocence, the more the Romulans will believe they're guilty because it's exactly what the Romulans would have done in their place. That's why you came to me, isn't it, Captain? Because you knew I could do those things that you weren't capable of doing. Well, it worked. And you'll get what you want, a war between the Romulans and the Dominion. And if your conscience is bothering you, you should soothe it with the knowledge that you may have just saved the entire Alpha Quadrant and all it cost was the life of one Romulan senator, one criminal, and the self-respect of one Starfleet officer. I don't know about you, but I'd call that a bargain.
[now in "Sisko's quarters"]
SISKO: At oh eight hundred hours, station time, the Romulan Empire formally declared war against the Dominion. They have already struck fifteen bases along the Cardassian border. So, this is a huge victory for the good guys. This may even be the turning point of the entire war. There's even a 'Welcome to the Fight' party tonight in the wardroom. So I lied, I cheated, I bribed men to cover the crimes of other men. I am an accessory to murder. But most damning thing of all, I think I can live with it. And if I had to do it all over again, I would. Garak was right about one thing. A guilty conscience is a small price to pay for the safety of the Alpha Quadrant, so I will learn to live with it. Because I can live with it. I can live with it. Computer, erase that entire personal log.
From Inter Arma Enim Silent Leges:
BASHIR: You don't see anything wrong with what happened, do you.
ROSS: I don't like it. But I've spent the last year and a half of my life ordering young men and young women to die. I like that even less.
(Bashir wakes to see -)
SLOAN: Good evening.
BASHIR: Are you expecting applause? Have you come to take a bow?
SLOAN: I just wanted to say thank you.
BASHIR: For what? Allowing you to manipulate me so completely?
SLOAN: For being a decent human being. That's why we selected you in the first place, Doctor. We needed somebody who wanted to play the game, but who would only go so far. When the time came, you stood your ground. You did the right thing. You reached out to an enemy, you told her the truth, you tried to stop a murder. The Federation needs men like you, Doctor. Men of conscience, men of principle, men who can sleep at night. You're also the reason Section Thirty one exists. Someone has to protect men like you from a universe that doesn't share your sense of right and wrong.
BASHIR: Should I feel sorry for you? Should I be weeping over the burden you're forced to carry in order to protect the rest of us?
SLOAN: It is an honour to know you, Doctor. Goodnight.
(Sloan leaves.)
BASHIR: Bashir to Security.
ODO [OC]: Odo here.
BASHIR: Never mind. My mistake.
To my mind, casting Section 31 as part of the system (calling them 'the good guys' is still a stretch, they're probably Lawful Neutral to Lawful Evil per standard 'spy' alignments. James Bond, IMF, Jason Bourne, A-Team, Team Weston from Burn Notice), means that the biggest, most important difference between them and the Tal-Shiar, Obsidian Order and even many modern spy agencies is that they seem to be primarily outward-focused, they keep a lookout for potential agents, maintain a watch/back-channels to top-level elements in friendly (and potentially non-friendly) governments, but for better than 99% of the Federation population (and virtually 100% of non-dependant civilians) S31 has no interest in them, and will never directly affect their lives.