Sisko was personally pissed at Eddington, not the Maquis personally. If anything Sisko wanted the Maquis to come in from the cold. That was NOT Javert's attitude. Javert would never have been able to forgive, let alone love Cassidy. Javert could never have tolerated having officers like Dax or Kira serving under him let alone Odo...who's sense of justice trumps his view of the law. Hell...Sisko tolerated Quark and Garak.
Sisko's issue with Eddington was personal. Not only did he betray Starfleet, he used and betrayed Sisko's trust.