It is definitely morally acceptable to kill enemy hackers, despite the virtual nature of their actions, precisely because their intent is to inflict harm on their enemy. It comes down to the simple adage "kill or be killed." Just because they are hackers does not mean they are peaceful, non-violent people. The information they obtain or the damage they inflict is meant to help their physical counterparts in the "real" war on the ground. They are not collateral damage but accessories to war, and therefore, are valid targets to be killed.
The odds are very strong that in this kind of war, there are going to be a lot of targets that are going to be attacked that disturb the way of life within the target. For example, hackers are likely going to target infrastructure, financial services, and medical services. All of these things are crucial in today's world to functioning societies, and they are still a direct threat to the health and safety of populaces if they are attacked.
While cyber warfare is conducted over the Internet, it is no less of an actual conflict than ground-based combat operations. To that end, the actual hackers and their physical locations are fair game. When we ping the location of a NOC (Network Operations Center) during a cyber attack, it should be the target of a coordinated bombing strike.
In a virtual battle between Enemy hackers and the US, cyber warfare is a real war. The enemy hackers should not be killed, as they live in other countries and are not terrorist. By killing hackers will activate a real war where people die, and though the hackers actions are not moral, they have not got a right to be killed.
We have a problem in society with the word war. We have a war on drugs, a war on poverty and a war on terror. However, simply calling something a war doesn't mean the rules of war apply. Cyber-warfare isn't actual warfare, and killing enemy hackers is simply not permissible. We are a nation of laws, and laws can deal with those who commit computer crimes.