did Sisko become a Javert, in His prosecution of the maquis, it seemed to me the entirety of starfleet did, might just be because I found myself ACTIVELY ROOTING for the alleged "bad guys"
Well, personally at least, I never got why Starfleet apparently never batted an eyelid at Sisko's use of a chemical weapon on the Maquis planet.
Starfleet cut Sisko's pay by 75% for several years
1. Noone was hurt - didn't even cause any environmental issues, most likely, as the Cardies from the planet Eddington gassed just moved there. Sure, it rendered the planet uninhabitable to human life, but the humans there had plenty of time to evacuate (and get a new world completely free from Cardassian occupation in the future!).
2. It most likely helped solidify Federation-Cardassian relations. Starfleet was pretty lax about doing stuff about the Maquis until Eddington's betrayal, which no doubt pissed the Cardassians off some, even with the newer, nicer civilian government. If the Cardies had the resources to divert from the Klingon effort, do you think they wouldn't have done the exact same thing Sisko did? If they didn't, it would be because they glassed the human colony instead of merely forcing them off the planet. The Cardassians finally saw a Starfleet captain with what it took to fight the Maquis.
3. Starfleet culture and morals aren't the same as Western 20-21st century morals - the Prime Directive is proof enough of that. Remember, Starfleet isn't just humans, so it makes sense that they might do things somewhat differently. And they do, even if it doesn't agree with how Our Heroes (with whom the audience is supposed to identify) view things - which we see often enough as well. Maybe some Vulcan JAG officer reviewing the case thought Sisko's actions were logical and justified, and dismissed the charges.