When civilization has been brought down due to nuclear holocaust, the whole idea of a "war crime" becomes rather outdated.

This is a simple question. There was no war, so there was no war crime. Beside, though the nuking of Megaton and subsequent death or ghoulification of every man, woman and child in the city is regarded as a tragedy, it was an important step in the establishment of the Super-Mirelurk/Enclave alliance, as it would assist the Lone Wanderer in establishing Project Purity by giving him a home base in Tenpenny Tower. The purification of the water which would lead to a sentient race of Mirelurks and the seeding of the first of the population of Super Mirelurks, our savior Mirelurk Overlords.