The purpose of Harris's speech is to argue, against the current postmodern fashion, that ethics and morality do in principle fall within the scientific domain, that there are ethical and moral truths to be found even if we cannot yet discern them. In response you mount a straw-man argument against a coarse implementation of utilitarian ethics, but this doesn't even relate to Harris's point.
To answer: yes, it would be a bad idea to kill all children found torturing small animals. Why? Because, as human beings, we would suffer greatly in such a society (to put it mildly, we find the notion of murdering our young unsettling, and children don't flourish into healthy adults in a society where their murder is considered acceptable), even if a naive implementation of utilitarian ethics incorrectly indicates that such an approach leads to the greatest overall happiness. That this is a fact subject to evidence, rather than a simple matter of opinion, is Harris's point here.