Because the Chantry was ultimately the driving force, the benevolent excuser of all the Templars’ misdeeds. The Chantry created the Templar. The Chantry created the rules about mages. Everything goes back to the Chantry, and Anders knew that and wanted to dismantle the very institution that was supporting the oppression. It sent a fairly strong message, I think. A supporter of the Chantry is a supporter of the mistreatment and imprisonment of mages.
I just wish there had been an option to hug him and pat him on the back for it. All they gave me was a range of rage to mild frustration.