Killing Innocent People Acceptable, Scalia States

In an amazing concurring opinion in Kansas v. Marsh, a death penalty case, Justice Scalia writes:

    Like other human institutions, courts and juries are not perfect. One cannot have a system of criminal punishment without accepting the possibility that someone will be punished mistakenly.

But in the case of the death penalty, a person isn't merely "punished."  The person is killed.  Isn't killing an innocent person murder? 

Perhaps it's the case that if you enact enough procedures to reduce the likelihood that an innocent person will be killed, then what you are doing is not really murder.  If so, what is killing a person under such circumstances called?

If a man scientist released a drug into the air that would only have a .01% chance of killing everyone who contacted it (and someone actually died), could that person be prosecuted for murder?  If not, why not?

I suppose the argument is that, unlike the mad scientist who need not release his toxins into the air, we must have a criminal justice system.  This is a fair point.  But does that mean our justice system must kill people?

Some might try a reductio ad absurdum, arguing that: "By your logic, we cannot have prisons, because wrongfully imprisoning someone is also a moral wrong."  However, I support prison reforms not because I care much about the dignity of the violent criminals, but because it is a fact that innocent people are in prison: The only way to mitigate the harm we as a society have done to the wrongfully imprisoned is to ensure they, at the very lease, are, say, able to avoid prison rape.  To do this, we must be over inclusive.  That is, since we know some people in prison are innocent, but we do not know which ones, we must enact measures that benefit everyone - even the guilty.

But back to my question.  Is it moral to have a system that kills innocent people .01% of the time?  If so, why?