Time to start working on the script for "Meat Hackers".

"Casualties of war" are, like it or not, a given. In war, if X is an active lethal threat, and the best expedient option is to destroy it ASAP, bystanders caught in the destruction are deemed acceptable losses. If a program running on your computer unbeknownst to you is doing something causing grave harm to others right now, those being harmed have the natural right to do whatever it takes, including at least equal harm, to make it stop.

In fact, that's the whole point of war: all other viable options for self-preservation (personal and national) have been exhausted, leaving only killing people and breaking things until the threat stops.

This is a problem of collecting evidence about who is responsible. It doesn't address the underlying nature of the responsibility. In your hypothetical, you are the one who is responsible both for the hacking of the military network (in the context of this discussion, presumably to do physical work like killing people) and for fingering someone else. This is indeed not very different from physically committing a murder and planting evidence pointing to someone else. Yet that does not cause us to challenge the notion of responsibility for murder.

If someone sneaks a bomb into your luggage and it goes off at the airport, didn't they just hijack your body to commit a crime?