It's understandable that Sisko would hate M.E. after being fooled by him but is this all just "a personal vendetta"? I mean, he's Starfleet. Wasn't his reaction part of Starfleet's, and /what/ was Starfleet like about the replicator incident? Wasn't there an investigation and a lot of unpleasant questions, like hey, your girlfriend is a Maquis, your ex-officer is a Maquis, wanna tell us something? If Sisko blamed those unpleasant moments on Eddington, his "obsession" would look so much clearer.
Yes, the issues between Michael Eddington and Captain Sisko are numerous and complex. I find Eddington’s repeated profession that “it’s not personal” to be not only ludicrous, but deliberately disingenuous. It’s very simple for the party who was never the target of personal attacks to claim “it’s not personal”, but that overlooks the fact that Eddington consistently used deeply intimate and personally significant information against Benjamin. Manipulating @kasidy-suggestion and specifically targeting her — out of all the other freighter captains he might have turned to if what he really needed had been food and medical supplies — solely because her involvement would prove the greatest distraction to the Captain is only the beginning. Throughout their encounters, Eddington never hesitated to wield whatever emotional and psychological weapons came to hand: the more personal, the better. His motives might not have been “personal”, but his methods unquestionably were.
Consider his assertion that the Federation is “worse than the Borg”, made to Benjamin after Eddington’s theft of the industrial replicators. He compared the Federation — the peace-driven and peace-keeping body of planets united by a dedication to freedom, civil rights, diplomacy, and exploration — to the brutal, conquering, monolithic enemy that killed Benjamin Sisko’s wife. Jennifer’s death is a matter of public record, and of common knowledge on Deep Space Nine. Eddington knowingly and deliberately ripped open that wound in a moment of triumph, simply to do more damage to a man he had already gored by manipulating the woman he had just learned to love. It was an incalculably cruel remark, and served no other purpose than to harm Ben more deeply than he’d already been harmed.
Another deeply personal, profoundly manipulative tactic Eddington used was the appeal to Benjamin’s love of children, forcing him at gunpoint to look at the displaced colonists in the caves on Marva IV. These colonists were driven from their by Cardassian forces, rather than evacuated with care and compassion by Federation vessels, because Eddington deluded innocent people into believing they could stand and fight against improbably odds. They were the victims of his grandiose fantasies, not of Starfleet, and yet Eddington attempted to twist that in order to strike at his former captain in yet another emotionally significant way — once again using knowledge of Ben’s nature that he’d gained under the guise of a subordinate and friend. Can anyone honestly say that’s not personal? Of course they can’t. It is.
Later still, Eddington deliberately brought up Cal Hudson in “casual” conversation, simply so that he could wound Benjamin with a barbed and accusatory account of his death at the hands of the Dominion. The implication was clear: that it was Ben, not the Jem’Hadar, who was in fact responsible. What kind of soulless person would bring someone news of a friend’s death in that way? And how, exactly, is that “not personal”?
Addressing your question more specifically, yes. Both Starfleet Intelligence and Internal Affairs investigated Captain Sisko thoroughly after Captain Yates’s conviction, weighing his involvement with the Maquis. Benjamin was already being watched closely because of his friendship with Cal Hudson and his expressed sympathies with the plight of Federation colonists in and near the Demlilitarized Zone. Kasidy’s involvement and the ease with which Eddington was able to deceive him (and by extension, all the rest of us) absolutely brought Ben under considerable scrutiny. He was ultimately absolved, but the gruelling nature of such an investigation always leaves a mark. I was interviewed three times myself in the course of this investigation, and those who testified to Benjamin’s loyalty and fitness for duty included First Minister Shakaar, Admiral Whatley, and the entire senior staff of Deep Space Nine. Though the investigation was closed and charges were never made, it remains a blight on Captain Sisko’s record, and a deep professional humiliation for an exemplary and loyal officer.
Furthermore, Starfleet Command was just as motivated to bring Michael Eddington to justice as anyone aboard the Defiant who hunted him down. There have been dozens of key Starfleet defectors to the Maquis — Lt. Cmdr Hudson, Lt. Paris, Ensign Ro, and others. But Lt. Cmdr. Eddington was of particular concern because of his close ties to Admiral Toddman, his position of considerable trust within Starfleet Security, and his charismatic influence that extended far beyond his single Maquis cell. He was a dangerous agitator, and did not represent the needs of the most vulnerable colonists. Ask @kira-suggestion how well the Maquis represented the interests of their Bajoran members, for instance.
As a Starfleet Captain, Benjamin Sisko had a duty to bring Eddington in before his dangerous and delusional behaviour sparked a war with Cardassia. The Central Command and later the Detapa Council did not diffferentiate between rogue humans, Vulcans, Betazoids, and other species from Federation worlds who had renounced their citizenship to persist as Maquis, and the Federation itself. They would have gone to war against all the worlds represented among the Maquis, Bajor included. Eddington had to be stopped. Captain Sisko did his duty in stopping him. We all did. The emotional and psychological cost of that mission weighs heavily on the crews of the Defiant and the Malinche, but we did what had to be done in an attempt to avert a war that would have cost millions, even billions of lives — all for the sake of one man’s ego.
So I have little patience for the argument that Eddington’s actions were justified, and NONE for the argument that they were not personal. They absolutely were. I don’t know why he chose to target the Captain so precisely. Perhaps to him, that was only a tactical decision, and a means to an end. But if he cannot see how his actions, his tactics, and above all his hateful words could be taken as personal by his victim, then there is certainly some merit to the JAG psychiatrist’s assessment that Eddington shows troubling signs of psychopathy. His continued assertions that his actions were “not personal” reflect more gravely upon him than upon any of us.
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