Eddington's switching sides wasn't particularly horrific either. He had no vendetta against Sisko and did what he did to support a cause he thought was right. The guy stole some replicators, which i'm sure the Federation would have easily replaced. Whilst Eddington also betrayed his oath and uniform That was never Sisko's motivation for going after him.
I know that no one died but whether people were killed is irrelevant to the point i'm trying to make. Sisko turned into a raving lunatic who poisoned a planet putting innocent lives at risk and initially displacing hundreds possibly thousands of people. He did this not because Eddington was a Maquis, but because Eddington bruised his ego and made him look like a fool.
He betrayed Sisko trust, that was bad enough.
A commanding officer believes he should trust the man under his command.
And Eddington did betray his Uniform. He did it by stealing from the Federation, he did it by attacking Federation ships, he did it the moment he used Biogenic warheads on a planet full of civilians and then crippled escaping Civilians fleeing from his unprovoked attack.
Which is a major difference.
These Cardarssian Colonist where the innocent party here. They took no part in what happened to the Marquis. They where just living their life when the Marquis attacked.
But hey , is Ok right. The Marquis are the underdogs, the good guys. So what if Cardarssian lives where uprooted and could have ended up dead. The Marquis are the true victims, they where betrayed by the Federation so it makes their act of Terrorism on a civilian Target all ok.
Because they where Cardies after all.
At least Sisko gave the Marquis a heads up.
As for Sisko turning into a raving loonie, he didn't really turn into one. He acted as he always has , what ever needs doing he did. But hey if Eddington wanted to play the gloating, holier then thou Rebel for a cause. Then to protect the peace Sisko was more then happy to play the villain .