Before the events of Waltz, Dukat really isn’t a clear cut bad guy. He is no Palpetine or Darth Vader. I agree since eventually he played the role of a bad guy, I mean he isn’t on the regular cast, you can say his role calls for a few victories over the heroes to keep the story interesting.
But within the given universe, Sisko never defeated Dukat. Dukat was on the verge of victory when Sisko had god like prophets to do him a favor and destroy the Dominion fleet coming through the Warmhole. The unexplainable defeat and watching his daughter die for no reason caused Dukat’s insanity.
After that, Dukat never again commended an army. After them being stranded on the same planet in Waltz, Sisko would not see Dukat again until the fire caves. By then, it was no longer about Tactics or Strategy.
The Dominion never had decisive man-power advantage when Dukat was in charge. Had the reinforcement not been wiped out by the Prophets, they would have, and the Dominion would sweep across the Alpha Quadrant.
When Dukat was still leading the Dominion war, Federation had Klingons as their allies. When Sisko took the fleet and charged Dominion line to retake DS9, Klingons haven’t arrived yet, that’s why the federation was out numbered at first. Once the Klingons arrived, they broke through the Dominion line.
Afterwards, Damar took over the Dominion war effort. Sisko took the combined force of Federation Klingons and Romulans and heads off with Dominion, Cardassians and the Breen. Two sides were equally matched. But due to the Breen’s energy drainning weapons, Sisko lost the battle and lost his own ship.
In the final battle Sisko was out numbered, until the Cardassians switched sides. But by that time, no Cardassian leader was in charge of the Dominion war effort. Dukat was on Bajor and on Pa’Wraith’s quest. Damar was leading the Cardassian resistance. And the new puppet was only in charge of putting down the resistance.
I wouldn’t say Eddington was desperate. Unlike other Maquis, he is not part of the DMZ refugees. He only joined the Maquis because he identifies with the Maquis cause. The really desperate Maquis were the likes of Cal Hudson early on in season 2. After Eddington joined the Maquis with the stolen Industrial Replicators, I think the Maquis did really well, especially since the Klingons invasion of Cardassia left the Maquis unchallenged in the DMZ.
When the Dominion wiped out the Maquis, that’s when Eddington was desperate. Still, at the end he had a certain swag and calm that truly defines Michael Eddington.
I don’t think betrayal gives ground for Sisko poisoning a planet just so that Eddington would surrender.
And yes, DS9 is great because it pushed the boundaries of Star Trek, but judging by what is presented, Sisko’s went out of his way to capture Eddington just because Eddington betrayed him, is in my eyes, a rather vein and pointless motive.
I think besides being angry at Eddington for fooled him, and used the security officer position under Sisko to steal federation industrial replicators, Sisko was more mad at Eddington for using Kasidy Yates to lure him away from DS9. In the end, Sisko had to send his lover to Federation prinson, and suffered bruised ego.
There have been others who betrayed Sisko, for example, Dukat betrayed Sisko more than once, yet you don’t see Sisko going out of his way to hunt down Dukat after Dukat stranded him on forsaken planet.
Morally, Sisko is as, if not more, shady as Eddington.