I think anyone who claims the Maquis were just defending their homes is forgetting that they also openly attacked both Cardassian and Federation ships and weren't above poisoning planets to get their way.
The Maquis that blew up Cardassian ships were Chakotay's Maquis. They were defending their homes because in "Maquis pt 1 & 2" we discovered that the Cardassians were supplying their citizens with weapons to terrorize the the Federation colonists left behind. At that time the Federation still considered the Maquis Federation citizens and was willing to pardon them as long as they stopped the hostilities. Remember, Sisko's friend Cal told him the Maquis had no beef with Starfleet/Federation and asked they be left alone because they didn't want to end up fighting their friends. Chakotay's Maquis were not enemies of the Federation.(or at least didn't want to be) Starfleet had to get involved because Cardassia told them if they didn't, they would and they'd kill them all. Remember officers like O'Brian sympathized with this group of Maquis.
It was Eddingtons leadership of the Maquis that made them go out and attack Federation ships and poison planets. He was due to his escalating matters is what caused Cardassia to seek out the help of the Dominion. To Dominion promised to kill all Maquis in return, Cardassia would become members of the Dominion. Nobody in Staerfleet sympathized with Eddingtons tactics and his direction of the Maquis. Due to his actions, his Maquis weren't welcomed or pardoned.
There are two different divisions of the Maquis, Chakotay's and Eddingtons.