I've said it before and I'll say it again. Sisko wasn't a perfect Star Fleet commander but he was the perfect Star Fleet commander for a frontier outpost like DS9. Any regulations and by the Academy officer would've been eaten alive by DS9, the station needed someone with the power of The Federation behind them while able to turn their back on certain necessary evils.

Also get his hands dirty too. It needed a Star Fleet officer who wasn't afraid to flip the switch during The Dominion Wars and utilize the military side of the peace force. It only cost him his humanity, but he sacrificed it to be the officer that would unleash human's capacity for savagery upon The Dominion, knowing it was the only way to defeat them.

It reminds me a bit of Murtry from Cibola Burns of The Expanse series, "We fly out here to this new place, and because we're civilized, we think civilization comes with us. It doesn't. We build it. And while we build it, a whole lot of people die. You think the American West came with railroads and post offices and jails? Those things were built, and at the cost of thousands of lives. They were built on the corpses of everyone who was there before the Spanish came. You don't get one without the other. And it's people like me who do it. People like you come later. All of this? This is because you showed up too early. Come back after I've built a post office and we'll talk." Murtry was a murdering psychopath but he wasn't entirely wrong either. The Federation is just another form of manifest destiny but at a grand scale. But instead of using muskets and murder, The Federation uses something much more insidious: politics. Sisko is charged with bringing The Federation's values and system of governance to the final frontier, and like most changing of the guard, it will cost bodies. Sisko is like Star Fleet's Murtry, someone like Picard is like Holden who comes later after we built a post office.