After last Sunday's lackluster hour, Falling Skies followed it up with the tense and revealing "Be Silent and Come Out." The eye-worm-controlled Hal wreaked havoc in Charleston, which led to a divide within the fighting forces.
Neither the 2nd Mass nor Charleston would be the strong force that it's become without the leadership of Tom Mason. Does that mean Tom and his family deserve special treatment? Perhaps, though it didn't really apply in this case.
Despite Pope's claims, Weaver would have treated any of "his" people the same way that he treated Hal if they were possessed and took Tom hostage. It wasn't that Hal was a Mason, but that he's one of the 2nd Mass. The fight has brought them together to form one large extended family of survivors with the Berserkers on the outside by their own choice.