We execute guilty murderers who have murdered innocent people.
For those who don't know the differrence between crime and punishment, guilty murderers and their innocent vicitms, this may be confusing.
For the rest of us, it is easy to understand.
The moral confusion exists when people blindly accept the amoral or immoral position that all killing is equal.
For those who believe all killing is morally equivalent, they would equate the slaughter of 6 million innocent Jews with the execution of those guilty murderers committing that slaughter. They would also equate the rape and murder of children with the execution of the rapist/murderer.
Fortunately, most folks really do know the difference.