I think personally it can be broken thusly...
Was Sisko a Javert.
A man obsessed over another petty crime vis a via stolen bread.
In the end regarding said original question, the answer is simply and undeniably no.
Eddington didn't steal bread. He was welcomed into Sisko home, feed. Trusted and expected to honor his duties as given.
He stole from said Home .
That's strike one.
He took action against the Federation, his uniform by tricking and crippling a Ship pursuring him for said crime.
Was it self defense , pretty much. But that could have gone wrong on so many ways. A wrong wire and dead Federation officers.
That's strike two.
He used a bio terrorist weapon on a defenceless target. And then crippled a refugee ship escaping said attack.
That folks is strike three
Sisko was no Javert to a harmless innocent who did a minor crime. He was however more then happy to play one to catch a man who can poison a planet and still clam moral authority.
If he brought a hammer to discipline a naughty child then he was a Javert. If he used the same tactics as his Eddington and played the villain then he was what happens when you decide to go around Bio nuking worlds.
If ya don't want to get mauled then don't poke the bear.