If you decide that your society is going to have a penal system, you know (since the system isn't perfect) that your system will inevitably punish innocent people. You can try to take measures to reduce that, but there's no way you can eliminate it. Nobody would say we shouldn't put a penal system into effect because it is wrong to harm innocent people for the greater good--even though harming innocent people for the greater good is exactly what it will do.
Sure. So we're sometimes willing to do some harm to innocents for the greater good. But if we were utilitarians we would always be thus willing. Civilized societies don't torture or execute their criminals, and wouldn't do so even if it was for the greater good.
The US has executions yet is otherwise considered civilized. So you must be claiming that the US is not civilized because it has executions, which makes it into a "no true Scotsman" argument.
Another month has passed and here is a new rationality quotes thread. The usual rules are: