DS9 "For The Uniform":
SISKO: Major, I want you to send the following message on all Maquis frequencies. To all the members of the Maquis resistance. This is Captain Sisko of the USS Defiant. In response to the Maquis's use of biogenic weapons in their recent attacks, I am about to take the following action. In exactly one hour, I will detonate two quantum torpedoes that will scatter trilithium resin in the atmosphere of Solosos Three. I thereby will make the planet uninhabitable to all human life for the next fifty years. I suggest evacuation plans begin immediately. What are you waiting for, people? Carry out your orders.
When Sisko makes this order he gets dissenting looks for everyone on the bridge and everyone freezes. That's why He yells at them "What are you waiting for people, carry out your orders."
(Later, orbiting Solosos Three.)
KIRA: Incoming message. It's Eddington.
EDDINGTON: (hologram) What are you really up to, Javert? Do you expect me to believe that a decorated Starfleet officer, the pride of the service, is going to poison an entire planet?
This is a very good question that Eddington asks Sisko. I've never heard of a Starfleet officer acting this way in an official matter.
SISKO: That's exactly what I'm going to do.
EDDINGTON: You're bluffing.
SISKO: Am I? Commander, launch torpedoes. Commander, I said launch torpedoes!
The reason he repeated himself is that Worf looked at Sisko like he was crazy and didn't fire them at first.
WORF: Aye, sir. (Two lights impact the atmosphere, and it starts turning yellow.)
KIRA: The trilithium resin is dissipating throughout the biosphere. The Maquis are scrambling their transport ships. They're starting to evacuate.
EDDINGTON: Do you realise what you've done?
SISKO: I've only just begun. I'm going to eliminate every Maquis colony in the DMZ.
EDDINGTON: You're talking about turning hundreds of thousands of people into homeless refugees.
Eddington frames the gravity of Sisko's actions and what Sisko plans to do. It would appear that if this is a viable option the Federation would have considered it.
SISKO: That's right. When you attacked the Malinche you proved one thing, that the Maquis have become an intolerable threat to the security of the Federation, and I am going intend to eliminate that threat.
Is that reason enough to take the action Sisko took.
EDDINGTON: But think about those people you saw in the caves, huddled and starving. They didn't attack the Malinche.
SISKO: You should have thought about that before you attacked a Federation starship. (Sisko turns his back on the Eddington hologram)
SISKO: Helm, lay in a course for Tracken Two, warp six. Commander, prepare two more torpedoes.
NOG: Engine Room, bridge. Warp six.
DAX: Set course zero five zero mark one seven nine.
WORF: Unlock safeties on torpedoes three and four.
EDDINGTON: Can't you see what's happening to you? You're going against everything you claim to believe in, and for what? To satisfy a personal vendetta?
SISKO: You betrayed your uniform!
EDDINGTON: And you're betraying yours right now! The sad part is, you don't even realise it. I feel sorry for you, Captain. This obsession with me, look what it's cost you.
This was clearly a personal vendetta. They weren't hunting the Maquis like this before or after. The Federation wouldn't shoot at human colonies destroying them or worse yet entire planets. Clearly that was unacceptable behavior or the Federation would have implemented that strategy from the get go and evacuated all the humans out of the Demilitarized zone and back to Federation space.
SISKO: Major, shut that thing off! Commander Worf, prepare to launch torpedoes!
EDDINGTON: Wait! If you call off your attack I'll turn over all our biogenic weapons.
SISKO: Not enough.
EDDINGTON: All right, Javert. I'll give you what you want. Me.
So it wasn't about the attacks or the Maquis, it was simply to bring Eddington back, who by the way committed no crime other then espionage to a non-enemy. It wasn't like Eddington was working for an enemy. Remember the Federation was not at war with the Maquis and the Maquis were not at war with the Federation.
DAX: Benjamin, I'm curious. Your plan to poison the Maquis planets. You didn't clear it with Starfleet first, did you.
SISKO: I knew I'd forgotten to do something.
DAX: Big gamble.
SISKO: That's what it takes to be a good villain.
Further he didn't clear it with Starfleet. And he was ordered earlier in the episode to not pursue Eddington, and was taken off the assignment.
Think about how hard it was for Picard to violate the prime directive to save people. He'd never do something so selfish. Even Worf who is a warrior and loves battle was shocked and at first hesitated to obey orders.
I've never heard of Starfleet firing at civilian targets. I've also never heard of Starfleet firing at a different target other than the one who has offended. This sort of strategy is something I would expect from the Romulans, Cardassians, Borg, Dominion, etc. not from Starfleet.
So my question is did Sisko's actions of firing at a planet inhabited by human colonists, for the purpose of making it uninhabitable, under the above scenario, violate Starfleet regulations or any Federation laws? If so is it a punishable offense. And if it is what was his punishment?