The federation makes peace with the cardassians; several federation colonies are in the vicinity of the demilitarized zone.
The cardassians keep breaking the treaty, killing federation colonists. The federation cheerfully lets this happen while doing nothing.
The colonists form the Maquis to fight back.
The federation savagely hunts down the Maquis.
Sisko, a starfleet captain, destroys 2 Maquis colonies (containing non-combatants, children, elderly) with only a low realistic chance of the inhabitants escaping their now destroyed home. That's a WAR CRIME by any legal definition.
The dominion attacks the Maquis colonies (which are still federation colonies - that's the justification given by starfleet for hunting them down; if the Maquis were independent, the federation would have no right to impose its jurisdiction on them), utterly destroying them. The federation cheerfully does nothing, despite it being clear that war with the dominion is imminent (Sisko mined the wormhole a few days/convoys later).
Yes, Sisko WAS a Javert. And a WAR CRIMINAL.
And the federation, starfleet and Sisko should be ashamed of their treatment of the Maquis. They proved themselves to be unworthy of loyalty. Indeed, any surviving Maquis is more than justified to view the federation as his/her proven enemy.