Does it really matter whether The Maquis were right or wrong to live where they were living? This episode was never about Sisko's view of The Maquis, it was about his view of one man who betrayed him, and the insane lengths he would go to have his ego sated.
Sisko poisoned two maquis colonies, potentially killing thousands of people if they could not evacuate in time all for the sake of sticking it to a guy who got the better of him. As much as i love The Sisko i could never agree with his actions and i think this episode conveniently gets forgotten whenever there is a 'sisko is better than janeway'/'sisko is the best captain' thread.
Janeway cops so much flak for her actions in 'equinox' Whilst her actions were unbecoming of a Starfleet Captain, she did it to stop a man who not only was killing an innocent alien species for fuel but had also attempted to murder her entire crew by taking the only protection they had.
Eddington was aiding the Maquis because of his own desire to be a hero and to support something he clearly believed was right. Eddington didn't join the maquis to spite sisko, yet sisko had to take it personally. So Eddington stole some replicators, the way sisko responded you would think the guy had killed Jake
Was sisko a javert? No, because from what i remember of les miserables, javert sounds a hell of a lot like odo and his need for order and justice. Sisko was not motivated by justice when he went after eddington it was ego fueled revenge.