All Human colonists were supposed to evacuate certain worlds in the DMZ as part of the treaty between the UFP and the Cardassians. Some colonists not only elected to remain behind, but also began a terrorist campaign against the Cardassians, which then prompted retaliatory strikes from Cardassia which in turn threatened to ignite a new war between Cardassia and the UFP. The Cardassian strikes were hitting innocent human settlements in addition to Maquis military camps, which forced the Fed to intercede. While not all the Maquis were living in Cardassian space, (some were in the DMZ and some were even on Federation worlds) the Cardassians certainly blamed the UFP for the Maquis raids just as the Feds blamed the Cardassian government for attacks perpetrated by Cardassian colonists.
That's the official rationale for the Fed campaign against the Maquis, but Eddington's statement that the real problem is that the Maquis have left the Federation and that *no one* leaves the Federation, has more than a kernel of truth in it. There's a sense of betrayal associated with the Maquis in the minds of the people in the Federation, regardless of whether that's an irrational feeling or not. Add to that sense of betrayal the fact that the Maquis have harassed and attacked several Federation targets over the years and you begin to see why the Feds refuse to turn a blind eye to this group.