Why did/do religions punish people so harshly for heresy?

Because religion wants control of the mes and any heresy is an act of rebellion. They didn't want the people to go against them because they would loose their power. Religion is the social structures that has done the most damage to humanity because of their indoctrination and brain-washing. Most people who did genocide were religious, and the churches themselves have done damage to society both physically and psychologically.